ALBERT

All Library Books, journals and Electronic Records Telegrafenberg

X
feed icon rss

Your email was sent successfully. Check your inbox.

An error occurred while sending the email. Please try again.

Proceed reservation?

Export
Filter
  • Public Library of Science  (118,249)
  • American Geophysical Union (AGU)
  • Annual Reviews
  • 2015-2019  (121,867)
  • 2000-2004  (5,910)
  • 1980-1984  (4,212)
  • 1935-1939  (289)
Collection
Keywords
Publisher
Years
Year
  • 1
    facet.materialart.
    Unknown
    Annual Acoustic Presence of Fin Whale (Balaenoptera physalus) Offshore Eastern Sicily, Central Mediterranean Sea (2016)
    Public Library of Science
    Details
    Publication Date: 2017-04-04
    Description: In recent years, an increasing number of surveys have definitively confirmed the seasonal presence of fin whales (Balaenoptera physalus) in highly productive regions of the Mediterranean Sea. Despite this, very little is yet known about the routes that the species seasonally follows within the Mediterranean basin and, particularly, in the Ionian area. The present study assesses for the first time fin whale acoustic presence offshore Eastern Sicily (Ionian Sea), throughout the processing of about 10 months of continuous acoustic monitoring. The recording of fin whale vocalizations was made possible by the cabled deep-sea multidisciplinary observatory, “NEMO-SN1”, deployed 25 km off the Catania harbor at a depth of about 2,100 meters. NEMO-SN1 is an operational node of the European Multidisciplinary Seafloor and water-column Observatory (EMSO) Research Infrastructure. The observatory was equipped with a low-frequency hydrophone (bandwidth: 0.05 Hz–1 kHz, sampling rate: 2 kHz) which continuously acquired data from July 2012 to May 2013. About 7,200 hours of acoustic data were analyzed by means of spectrogram display. Calls with the typical structure and patterns associated to the Mediterranean fin whale population were identified and monitored in the area for the first time. Furthermore, a background noise analysis within the fin whale communication frequency band (17.9–22.5 Hz) was conducted to investigate possible detection-masking effects. The study confirms the hypothesis that fin whales are present in the Ionian Sea throughout all seasons, with peaks in call detection rate during spring and summer months. The analysis also demonstrates that calls were more frequently detected in low background noise conditions. Further analysis will be performed to understand whether observed levels of noise limit the acoustic detection of the fin whales vocalizations, or whether the animals vocalize less in the presence of high background noise.
    Description: Published
    Description: e0141838
    Description: 3A. Ambiente Marino
    Description: JCR Journal
    Description: open
    Keywords: Whales ; Bioacoustics ; Background noise (acoustics) ; Acoustic signals ; Sperm whales ; Vocalization ; Acoustics ; Data acquisition ; 03. Hydrosphere::03.01. General::03.01.08. Instruments and techniques ; 03. Hydrosphere::03.02. Hydrology::03.02.04. Measurements and monitoring ; 03. Hydrosphere::03.02. Hydrology::03.02.07. Instruments and techniques ; 03. Hydrosphere::03.04. Chemical and biological::03.04.99. General or miscellaneous
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 2
    facet.materialart.
    Unknown
    Temperature-induced viral resistance in Emiliania huxleyi (Prymnesiophyceae) (2015)
    Public Library of Science
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e112134, doi:10.1371/journal.pone.0112134.
    Description: Annual Emiliania huxleyi blooms (along with other coccolithophorid species) play important roles in the global carbon and sulfur cycles. E. huxleyi blooms are routinely terminated by large, host-specific dsDNA viruses, (Emiliania huxleyi Viruses; EhVs), making these host-virus interactions a driving force behind their potential impact on global biogeochemical cycles. Given projected increases in sea surface temperature due to climate change, it is imperative to understand the effects of temperature on E. huxleyi’s susceptibility to viral infection and its production of climatically active dimethylated sulfur species (DSS). Here we demonstrate that a 3°C increase in temperature induces EhV-resistant phenotypes in three E. huxleyi strains and that successful virus infection impacts DSS pool sizes. We also examined cellular polar lipids, given their documented roles in regulating host-virus interactions in this system, and propose that alterations to membrane-bound surface receptors are responsible for the observed temperature-induced resistance. Our findings have potential implications for global biogeochemical cycles in a warming climate and for deciphering the particular mechanism(s) by which some E. huxleyi strains exhibit viral resistance.
    Description: This study was supported by funding from the National Science Foundation (OCE-1061883 to KDB, BVM, and OCE-1061876 to GRD) and in part by grants from The Gordon and Betty Moore Foundation (to BVM and KDB).
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
    Format: image/tiff
    Format: application/vnd.ms-excel
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 3
    facet.materialart.
    Unknown
    Protist community grazing on prokaryotic prey in deep ocean water masses (2015)
    Public Library of Science
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 10 (2015): e0124505, doi:10.1371/journal.pone.0124505.
    Description: Oceanic protist grazing at mesopelagic and bathypelagic depths, and their subsequent effects on trophic links between eukaryotes and prokaryotes, are not well constrained. Recent studies show evidence of higher than expected grazing activity by protists down to mesopelagic depths. This study provides the first exploration of protist grazing in the bathypelagic North Atlantic Deep Water (NADW). Grazing was measured throughout the water column at three stations in the South Atlantic using fluorescently-labeled prey analogues. Grazing in the deep Antarctic Intermediate water (AAIW) and NADW at all three stations removed 3.79% ± 1.72% to 31.14% ± 8.24% of the standing prokaryote stock. These results imply that protist grazing may be a significant source of labile organic carbon at certain meso- and bathypelagic depths.
    Description: Funding for the cruise was provided by the National Science Foundation (OCE-1154320) to EBK. Funding for the laboratory work was provided by contributions from the Woods Hole Oceanographic Institution Director of Research, Ocean Life Institute, and Deep Ocean Exploration Institute to VE.
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 4
    facet.materialart.
    Unknown
    Exploration of the canyon-incised continental margin of the northeastern United States reveals dynamic habitats and diverse communities (2015)
    Public Library of Science
    Details
    Publication Date: 2022-05-25
    Description: This is an open access article, free of all copyright. The definitive version was published in PLoS One 10 (2015): e0139904, doi: 10.1371/journal.pone.0139904.
    Description: The continental margin off the northeastern United States (NEUS) contains numerous, topographically complex features that increase habitat heterogeneity across the region. However, the majority of these rugged features have never been surveyed, particularly using direct observations. During summer 2013, 31 Remotely-Operated Vehicle (ROV) dives were conducted from 494 to 3271 m depth across a variety of seafloor features to document communities and to infer geological processes that produced such features. The ROV surveyed six broad-scale habitat features, consisting of shelf-breaching canyons, slope-sourced canyons, inter-canyon areas, open-slope/landslide-scar areas, hydrocarbon seeps, and Mytilus Seamount. Four previously unknown chemosynthetic communities dominated by Bathymodiolus mussels were documented. Seafloor methane hydrate was observed at two seep sites. Multivariate analyses indicated that depth and broad-scale habitat significantly influenced megafaunal coral (58 taxa), demersal fish (69 taxa), and decapod crustacean (34 taxa) assemblages. Species richness of fishes and crustaceans significantly declined with depth, while there was no relationship between coral richness and depth. Turnover in assemblage structure occurred on the middle to lower slope at the approximate boundaries of water masses found previously in the region. Coral species richness was also an important variable explaining variation in fish and crustacean assemblages. Coral diversity may serve as an indicator of habitat suitability and variation in available niche diversity for these taxonomic groups. Our surveys added 24 putative coral species and three fishes to the known regional fauna, including the black coral Telopathes magna, the octocoral Metallogorgia melanotrichos and the fishes Gaidropsarus argentatus, Guttigadus latifrons, and Lepidion guentheri. Marine litter was observed on 81% of the dives, with at least 12 coral colonies entangled in debris. While initial exploration revealed the NEUS region to be both geologically dynamic and biologically diverse, further research into the abiotic conditions and the biotic interactions that influence species abundance and distribution is needed.
    Description: Funding for the ship and ROV time was provided by NOAA’s Office of Ocean Exploration and Research with support from NOAA’s Deep Sea Coral Research and Technology Program, Northeast Initiative.
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 5
    facet.materialart.
    Unknown
    The amyloid precursor protein of Alzheimer’s disease clusters at the organelle/microtubule interface on organelles that bind microtubules in an ATP dependent manner (2016)
    Public Library of Science
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 11 (2016): e0147808, doi:10.1371/journal.pone.0147808.
    Description: The amyloid precursor protein (APP) is a causal agent in the pathogenesis of Alzheimer’s disease and is a transmembrane protein that associates with membrane-limited organelles. APP has been shown to co-purify through immunoprecipitation with a kinesin light chain suggesting that APP may act as a trailer hitch linking kinesin to its intercellular cargo, however this hypothesis has been challenged. Previously, we identified an mRNA transcript that encodes a squid homolog of human APP770. The human and squid isoforms share 60% sequence identity and 76% sequence similarity within the cytoplasmic domain and share 15 of the final 19 amino acids at the C-terminus establishing this highly conserved domain as a functionally import segment of the APP molecule. Here, we study the distribution of squid APP in extruded axoplasm as well as in a well-characterized reconstituted organelle/microtubule preparation from the squid giant axon in which organelles bind microtubules and move towards the microtubule plus-ends. We find that APP associates with microtubules by confocal microscopy and co-purifies with KI-washed axoplasmic organelles by sucrose density gradient fractionation. By electron microscopy, APP clusters at a single focal point on the surfaces of organelles and localizes to the organelle/microtubule interface. In addition, the association of APP-organelles with microtubules is an ATP dependent process suggesting that the APP-organelles contain a microtubule-based motor protein. Although a direct kinesin/APP association remains controversial, the distribution of APP at the organelle/microtubule interface strongly suggests that APP-organelles have an orientation and that APP like the Alzheimer’s protein tau has a microtubule-based function.
    Description: Research reported in this publication was supported by an Institutional Development Award (IDeA) from the National Institute of General Medical Sciences of the National Institutes of Health under grant number P20GM103430.
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 6
    facet.materialart.
    Unknown
    Influence of environmental variables on Gambierdiscus spp. (Dinophyceae) growth and distribution (2016)
    Public Library of Science
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 11 (2016): e0153197, doi:10.1371/journal.pone.0153197.
    Description: Benthic dinoflagellates in the genus Gambierdiscus produce the ciguatoxin precursors responsible for the occurrence of ciguatera toxicity. The prevalence of ciguatera toxins in fish has been linked to the presence and distribution of toxin-producing species in coral reef ecosystems, which is largely determined by the presence of suitable benthic habitat and environmental conditions favorable for growth. Here using single factor experiments, we examined the effects of salinity, irradiance, and temperature on growth of 17 strains of Gambierdiscus representing eight species/phylotypes (G. belizeanus, G. caribaeus, G. carolinianus, G. carpenteri, G. pacificus, G. silvae, Gambierdiscus sp. type 4–5), most of which were established from either Marakei Island, Republic of Kiribati, or St. Thomas, United States Virgin Island (USVI). Comparable to prior studies, growth rates fell within the range of 0–0.48 divisions day-1. In the salinity and temperature studies, Gambierdiscus responded in a near Gaussian, non-linear manner typical for such studies, with optimal and suboptimal growth occurring in the range of salinities of 25 and 45 and 21.0 and 32.5°C. In the irradiance experiment, no mortality was observed; however, growth rates at 55μmol photons · m-2 · s-1 were lower than those at 110–400μmol photons · m-2 · s-1. At the extremes of the environmental conditions tested, growth rates were highly variable, evidenced by large coefficients of variability. However, significant differences in intraspecific growth rates were typically found only at optimal or near-optimal growth conditions. Polynomial regression analyses showed that maximum growth occurred at salinity and temperature levels of 30.1–38.5 and 23.8–29.2°C, respectively. Gambierdiscus growth patterns varied among species, and within individual species: G. belizeanus, G. caribaeus, G. carpenteri, and G. pacificus generally exhibited a wider range of tolerance to environmental conditions, which may explain their broad geographic distribution. In contrast, G. silvae and Gambierdiscus sp. types 4–5 all displayed a comparatively narrow range of tolerance to temperature, salinity, and irradiance.
    Description: This study was funded by the National Natural Science Foundation of China (41506137); Guangxi Natural Science Foundation (2015GXNSFCA139003), Centers for Disease Control and Prevention (U01 EH000421); USFDA (F223201000060C); NOAA NOS through the CiguaHAB program (Cooperative Agreement NA11NOS4780060, NA11NOS4780028); the Lana Vento Trust and VI-EPSCoR Program (NSF award # 346483 & 081441); and a System Fund from Key Laboratory of Environment Change and Resources Use in Beibu Gulf, Ministry of Education (2014BGERLXT01). Support was also provided by the Woods Hole Center for Oceans and Human Health through National Science Foundation (NSF) Grant OCE-1314642, National Institute of Environmental Health Sciences (NIEHS) Grant 1-P01-ES021923-014, as well as the China Scholarship Council.
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 7
    facet.materialart.
    Unknown
    Comparative analysis of secretome profiles of manganese(II)-oxidizing Ascomycete fungi (2016)
    Public Library of Science
    Details
    Publication Date: 2022-05-25
    Description: This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose.
    Description: Fungal secretomes contain a wide range of hydrolytic and oxidative enzymes, including cellulases, hemicellulases, pectinases, and lignin-degrading accessory enzymes, that synergistically drive litter decomposition in the environment. While secretome studies of model organisms such as Phanerochaete chrysosporium and Aspergillus species have greatly expanded our knowledge of these enzymes, few have extended secretome characterization to environmental isolates or conducted side-by-side comparisons of diverse species. Thus, the mechanisms of carbon degradation by many ubiquitous soil fungi remain poorly understood. Here we use a combination of LC-MS/MS, genomic, and bioinformatic analyses to characterize and compare the protein composition of the secretomes of four recently isolated, cosmopolitan, Mn(II)-oxidizing Ascomycetes (Alternaria alternata SRC1lrK2f, Stagonospora sp. SRC1lsM3a, Pyrenochaeta sp. DS3sAY3a, and Paraconiothyrium sporulosum AP3s5-JAC2a). We demonstrate that the organisms produce a rich yet functionally similar suite of extracellular enzymes, with species-specific differences in secretome composition arising from unique amino acid sequences rather than overall protein function. Furthermore, we identify not only a wide range of carbohydrate-active enzymes that can directly oxidize recalcitrant carbon, but also an impressive suite of redox-active accessory enzymes that suggests a role for Fenton-based hydroxyl radical formation in indirect, non-specific lignocellulose attack. Our findings highlight the diverse oxidative capacity of these environmental isolates and enhance our understanding of the role of filamentous Ascomycetes in carbon turnover in the environment.
    Description: This work was supported by the National Science Foundation (www.nsf.gov), grant numbers EAR-1249489 and CBET-1336496, both awarded to CMH. Personal support for CAZ was also provided by Harvard University (www.harvard.edu) and by a Ford Foundation (www.fordfoundation.org) Predoctoral Fellowship administered by the National Academies.
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 8
    facet.materialart.
    Unknown
    Potential impacts of offshore wind farms on North Sea stratification (2016)
    Public Library of Science
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 11 (2016): e0160830, doi:10.1371/journal.pone.0160830 .
    Description: Advances in offshore wind farm (OWF) technology have recently led to their construction in coastal waters that are deep enough to be seasonally stratified. As tidal currents move past the OWF foundation structures they generate a turbulent wake that will contribute to a mixing of the stratified water column. In this study we show that the mixing generated in this way may have a significant impact on the large-scale stratification of the German Bight region of the North Sea. This region is chosen as the focus of this study since the planning of OWFs is particularly widespread. Using a combination of idealised modelling and in situ measurements, we provide order-of-magnitude estimates of two important time scales that are key to understanding the impacts of OWFs: (i) a mixing time scale, describing how long a complete mixing of the stratification takes, and (ii) an advective time scale, quantifying for how long a water parcel is expected to undergo enhanced wind farm mixing. The results are especially sensitive to both the drag coefficient and type of foundation structure, as well as the evolution of the pycnocline under enhanced mixing conditions—both of which are not well known. With these limitations in mind, the results show that OWFs could impact the large-scale stratification, but only when they occupy extensive shelf regions. They are expected to have very little impact on large-scale stratification at the current capacity in the North Sea, but the impact could be significant in future large-scale development scenarios.
    Description: Funding was provided by the Helmholtz Foundation through the Polar Regions and Coasts in the Changing Earth System II (PACES II) program.
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 9
    facet.materialart.
    Unknown
    Predicting interactions between common dolphins and the pole-and-line tuna fishery in the Azores (2016)
    Public Library of Science
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 11 (2016): e0164107, doi:10.1371/journal.pone.0164107.
    Description: Common dolphins (Delphinus delphis) are responsible for the large majority of interactions with the pole-and-line tuna fishery in the Azores but the underlying drivers remain poorly understood. In this study we investigate the influence of various environmental and fisheries-related factors in promoting the interaction of common dolphins with this fishery and estimate the resultant catch losses. We analysed 15 years of fishery and cetacean interaction data (1998–2012) collected by observers placed aboard tuna fishing vessels. Dolphins interacted in less than 3% of the fishing events observed during the study period. The probability of dolphin interaction varied significantly between years with no evident trend over time. Generalized additive modeling results suggest that fishing duration, sea surface temperature and prey abundance in the region were the most important factors explaining common dolphin interaction. Dolphin interaction had no impact on the catches of albacore, skipjack and yellowfin tuna but resulted in significantly lower catches of bigeye tuna, with a predicted median annual loss of 13.5% in the number of fish captured. However, impact on bigeye catches varied considerably both by year and fishing area. Our work shows that rates of common dolphin interaction with the pole-and-line tuna fishery in the Azores are low and showed no signs of increase over the study period. Although overall economic impact was low, the interaction may lead to significant losses in some years. These findings emphasize the need for continued monitoring and for further research into the consequences and economic viability of potential mitigation measures.
    Description: This work was funded by Fundação para a Ciência e a Tecnologia (FCT) and DRCT/SRCTE, though FEDER, the Competitiveness Factors Operational (COMPETE), QREN European Social Fund, the Portuguese Ministry for Science and Education, under research projects TRACE (PTDC/MAR/74071/2006), FCT Exploratory Project (IF/00943/2013/CP1199/CT0001), and MAPCET (M2.1.2/F/012/2011). We acknowledge the support of Fundação para a Ciência e Tecnologia (FCT), through the strategic project UID/MAR/04292/2013 granted to MARE. We thank the Azorean Regional Government for funding POPA, the Ship-owners Association and the Association of the Tuna Canning Industries for their support to the program. MJC was supported by a DRCT doctoral grant (M3.1.2/F/008/2009). MAS was supported by POPH, QREN, European Social Fund and Portuguese Ministry for Science and Education, through an FCT Investigator grant (IF/00943/2013).
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 10
    facet.materialart.
    Unknown
    Light control of G protein signaling pathways by a novel photopigment (2018)
    Public Library of Science
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 13 (2018): e0205015, doi:10.1371/journal.pone.0205015.
    Description: Channelopsins and photo-regulated ion channels make it possible to use light to control electrical activity of cells. This powerful approach has lead to a veritable explosion of applications, though it is limited to changing membrane voltage of the target cells. An enormous potential could be tapped if similar opto-genetic techniques could be extended to the control of chemical signaling pathways. Photopigments from invertebrate photoreceptors are an obvious choice—as they do not bleach upon illumination -however, their functional expression has been problematic. We exploited an unusual opsin, pScop2, recently identified in ciliary photoreceptors of scallop. Phylogenetically, it is closer to vertebrate opsins, and offers the advantage of being a bi-stable photopigment. We inserted its coding sequence and a fluorescent protein reporter into plasmid vectors and demonstrated heterologous expression in various mammalian cell lines. HEK 293 cells were selected as a heterologous system for functional analysis, because wild type cells displayed the largest currents in response to the G-protein activator, GTP-γ-S. A line of HEK cells stably transfected with pScop2 was generated; after reconstitution of the photopigment with retinal, light responses were obtained in some cells, albeit of modest amplitude. In native photoreceptors pScop2 couples to Go; HEK cells express poorly this G-protein, but have a prominent Gq/PLC pathway linked to internal Ca mobilization. To enhance pScop2 competence to tap into this pathway, we swapped its third intracellular loop—important to confer specificity of interaction between 7TMDRs and G-proteins—with that of a Gq-linked opsin which we cloned from microvillar photoreceptors present in the same retina. The chimeric construct was evaluated by a Ca fluorescence assay, and was shown to mediate a robust mobilization of internal calcium in response to illumination. The results project pScop2 as a potentially powerful optogenetic tool to control signaling pathways.
    Description: This work was funded by Colciencias grant FP44842-010-2015 and Connecticut Fund for Science.
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 11
    facet.materialart.
    Unknown
    Petrocarbon evolution: Ramped pyrolysis/oxidation and isotopic studies of contaminated oil sediments from the Deepwater Horizon oil spill in the Gulf of Mexico. (2019)
    Public Library of Science
    Details
    Publication Date: 2022-05-25
    Description: © The Authors, 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Rogers, K. L., Bosman, S. H., Lardie-Gaylord, M., McNichol, A., Rosenheim, B. E., Montoya, J. P., & Chanton, J. P. (2019). Petrocarbon evolution: Ramped pyrolysis/oxidation and isotopic studies of contaminated oil sediments from the Deepwater Horizon oil spill in the Gulf of Mexico. PLoS One, 14(2), (2019):e0212433, doi:10.1371/journal.pone.0212433.
    Description: Hydrocarbons released during the Deepwater Horizon (DWH) oil spill weathered due to exposure to oxygen, light, and microbes. During weathering, the hydrocarbons’ reactivity and lability was altered, but it remained identifiable as “petrocarbon” due to its retention of the distinctive isotope signatures (14C and 13C) of petroleum. Relative to the initial estimates of the quantity of oil-residue deposited in Gulf sediments based on 2010–2011 data, the overall coverage and quantity of the fossil carbon on the seafloor has been attenuated. To analyze recovery of oil contaminated deep-sea sediments in the northern Gulf of Mexico we tracked the carbon isotopic composition (13C and 14C, radiocarbon) of bulk sedimentary organic carbon through time at 4 sites. Using ramped pyrolysis/oxidation, we determined the thermochemical stability of sediment organic matter at 5 sites, two of these in time series. There were clear differences between crude oil (which decomposed at a lower temperature during ramped oxidation), natural hydrocarbon seep sediment (decomposing at a higher temperature; Δ14C = -912‰) and our control site (decomposing at a moderate temperature; Δ14C = -189‰), in both the stability (ability to withstand ramped temperatures in oxic conditions) and carbon isotope signatures. We observed recovery toward our control site bulk Δ14C composition at sites further from the wellhead in ~4 years, whereas sites in closer proximity had longer recovery times. The thermographs also indicated temporal changes in the composition of contaminated sediment, with shifts towards higher temperature CO2 evolution over time at a site near the wellhead, and loss of higher temperature CO2 peaks at a more distant site.
    Description: This research was made possible by grants from The Gulf of Mexico Research Initiative through its consortiums: Ecosystem Impacts of Oil & Gas Inputs to the Gulf (ECOGIG), The Center for the Integrated Modeling and Analysis of the Gulf Ecosystem (C-Image), and Deep Sea to Coast Connectivity in the Eastern Gulf of Mexico (Deep-C) and the Resuspension, Redistribution and Deposition of DWH Recalcitrant Material (Re-Direct) project. This is ECOGIG Contribution # 521. Funding was also provided by the National Ocean Sciences Accelerator Mass Spectrometry Facility (NOSAMS) Graduate Student Internship Program (NSF OCE-1239667). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 12
    facet.materialart.
    Unknown
    Microbial iron mats at the Mid-Atlantic Ridge and evidence that Zetaproteobacteria may be restricted to iron-oxidizing marine systems (2015)
    Public Library of Science
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 10 (2015): e0119284, doi:10.1371/journal.pone.0119284 .
    Description: Chemolithoautotrophic iron-oxidizing bacteria play an essential role in the global iron cycle. Thus far, the majority of marine iron-oxidizing bacteria have been identified as Zetaproteobacteria, a novel class within the phylum Proteobacteria. Marine iron-oxidizing microbial communities have been found associated with volcanically active seamounts, crustal spreading centers, and coastal waters. However, little is known about the presence and diversity of iron-oxidizing communities at hydrothermal systems along the slow crustal spreading center of the Mid-Atlantic Ridge. From October to November 2012, samples were collected from rust-colored mats at three well-known hydrothermal vent systems on the Mid-Atlantic Ridge (Rainbow, Trans-Atlantic Geotraverse, and Snake Pit) using the ROV Jason II. The goal of these efforts was to determine if iron-oxidizing Zetaproteobacteria were present at sites proximal to black smoker vent fields. Small, diffuse flow venting areas with high iron(II) concentrations and rust-colored microbial mats were observed at all three sites proximal to black smoker chimneys. A novel, syringe-based precision sampler was used to collect discrete microbial iron mat samples at the three sites. The presence of Zetaproteobacteria was confirmed using a combination of 16S rRNA pyrosequencing and single-cell sorting, while light micros-copy revealed a variety of iron-oxyhydroxide structures, indicating that active iron-oxidizing communities exist along the Mid-Atlantic Ridge. Sequencing analysis suggests that these iron mats contain cosmopolitan representatives of Zetaproteobacteria, but also exhibit diversity that may be uncommon at other iron-rich marine sites studied to date. A meta-analysis of publically available data encompassing a variety of aquatic habitats indicates that Zetaproteobacteria are rare if an iron source is not readily available. This work adds to the growing understanding of Zetaproteobacteria ecology and suggests that this organism is likely locally restricted to iron-rich marine environments but may exhibit wide-scale geographic distribution, further underscoring the importance of Zetaproteobacteria in global iron cycling.
    Description: This work was supported by grants from the National Science Foundation [grants OCE-0926805 (DE and JAB), OCE-1155754 (DE), and OCE-1131109 (GWL)] and the National Aeronautics and Space Administration [NNX12AG20G (GWL and DE)].
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 13
    facet.materialart.
    Unknown
    Microbial gene abundance and expression patterns across a river to ocean salinity gradient (2015)
    Public Library of Science
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 10 (2015): e0140578, doi: 10.1371/journal.pone.0140578.
    Description: Microbial communities mediate the biogeochemical cycles that drive ecosystems, and it is important to understand how these communities are affected by changing environmental conditions, especially in complex coastal zones. As fresh and marine waters mix in estuaries and river plumes, the salinity, temperature, and nutrient gradients that are generated strongly influence bacterioplankton community structure, yet, a parallel change in functional diversity has not been described. Metagenomic and metatranscriptomic analyses were conducted on five water samples spanning the salinity gradient of the Columbia River coastal margin, including river, estuary, plume, and ocean, in August 2010. Samples were pre-filtered through 3 μm filters and collected on 0.2 μm filters, thus results were focused on changes among free-living microbial communities. Results from metagenomic 16S rRNA sequences showed taxonomically distinct bacterial communities in river, estuary, and coastal ocean. Despite the strong salinity gradient observed over sampling locations (0 to 33), the functional gene profiles in the metagenomes were very similar from river to ocean with an average similarity of 82%. The metatranscriptomes, however, had an average similarity of 31%. Although differences were few among the metagenomes, we observed a change from river to ocean in the abundance of genes encoding for catabolic pathways, osmoregulators, and metal transporters. Additionally, genes specifying both bacterial oxygenic and anoxygenic photosynthesis were abundant and expressed in the estuary and plume. Denitrification genes were found throughout the Columbia River coastal margin, and most highly expressed in the estuary. Across a river to ocean gradient, the free-living microbial community followed three different patterns of diversity: 1) the taxonomy of the community changed strongly with salinity, 2) metabolic potential was highly similar across samples, with few differences in functional gene abundance from river to ocean, and 3) gene expression was highly variable and generally was independent of changes in salinity.
    Description: This study was carried out within the context of the Science and Technology Center for Coastal Margin Observation & Prediction (CMOP) supported by the National Science Foundation, grant number OCE-0424602 to Antonio Baptista (http://www.stccmop.org).
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
    Format: text/plain
    Format: application/vnd.ms-excel
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 14
    facet.materialart.
    Unknown
    Mercury-pollution induction of intracellular lipid accumulation and lysosomal compartment amplification in the benthic foraminifer Ammonia parkinsoniana (2016)
    Public Library of Science
    Details
    Publication Date: 2022-05-25
    Description: This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The definitive version was published in PLoS One 11 (2016): e0162401, doi:10.1371/journal.pone.0162401.
    Description: Heavy metals such as mercury (Hg) pose a significant health hazard through bioaccumulation and biomagnification. By penetrating cell membranes, heavy metal ions may lead to pathological conditions. Here we examined the responses of Ammonia parkinsoniana, a benthic foraminiferan, to different concentrations of Hg in the artificial sea water. Confocal images of untreated and treated specimens using fluorescent probes (Nile Red and Acridine Orange) provided an opportunity for visualizing the intracellular lipid accumulation and acidic compartment regulation. With increased Hg over time, we observed an increased number of lipid droplets, which may have acted as a detoxifying organelle where Hg is sequestered and biologically inactivated. Further, Hg seems to promote the proliferation of lysosomes both in terms of number and dimension that, at the highest level of Hg, resulted in cell death. We report, for the first time, the presence of Hg within the foraminiferal cell: at the basal part of pores, in the organic linings of the foramen/septa, and as cytoplasmic accumulations.
    Description: The research for this paper was partially made possible by the financial support from the PRIN 2010-2011 Ministero dell’Istruzione, dell’Università e della Ricerca (MIUR) (protocollo 2010RMTLYR) to RC. JMB acknowledges support from The Investment in Science Fund at WHOI. BG, JRE, AJ, LZ, and EMP were supported in part by the Office of Biological and Environmental Research, US Department of Energy (DOE) as part of the Mercury Science Focus Area at Oak Ridge National Laboratory, which is managed by UT-Battelle LLC for the DOE under contract DE-AC05-00OR22725.
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 15
    facet.materialart.
    Unknown
    Shipboard design and fabrication of custom 3D-printed soft robotic manipulators for the investigation of delicate deep-sea organisms (2018)
    Public Library of Science
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLos One 13 (2018): e0200386, doi:10.1371/journal.pone.0200386.
    Description: Soft robotics is an emerging technology that has shown considerable promise in deep-sea marine biological applications. It is particularly useful in facilitating delicate interactions with fragile marine organisms. This study describes the shipboard design, 3D printing and integration of custom soft robotic manipulators for investigating and interacting with deep-sea organisms. Soft robotics manipulators were tested down to 2224m via a Remotely-Operated Vehicle (ROV) in the Phoenix Islands Protected Area (PIPA) and facilitated the study of a diverse suite of soft-bodied and fragile marine life. Instantaneous feedback from the ROV pilots and biologists allowed for rapid re-design, such as adding “fingernails”, and re-fabrication of soft manipulators at sea. These were then used to successfully grasp fragile deep-sea animals, such as goniasterids and holothurians, which have historically been difficult to collect undamaged via rigid mechanical arms and suction samplers. As scientific expeditions to remote parts of the world are costly and lengthy to plan, on-the-fly soft robot actuator printing offers a real-time solution to better understand and interact with delicate deep-sea environments, soft-bodied, brittle, and otherwise fragile organisms. This also offers a less invasive means of interacting with slow-growing deep marine organisms, some of which can be up to 18,000 years old.
    Description: This work is supported by NOAA OER Grant # NA17OAR0110083 “Exploration of the Seamounts of the Phoenix Islands Protected Area” to RDR, EEC, TMS and DFG and Schmidt Ocean Institute Grant: “What is the Current State of the Deep-Sea Coral Ecosystem in the Phoenix Island Protected Area?” to EEC, RDR, TMS and DFG; NSF Instrument Development for Biological Research Award # 1556164 to RJW and #1556123 to DFG; the National Academies Keck Futures Initiative of the National Academy of Sciences under award #NAKFI DBS21 to RJW and DFG; and NFS Research Fellowship awarded to KPB (#DGE1144152). It is also supported by the Wyss Institute for Biologically Inspired Engineering at Harvard University. We are grateful for the support from the National Geographic Society Innovation Challenge (Grant No.: SP 12-14) to RJW and DFG.
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 16
    facet.materialart.
    Unknown
    Resonance control of acoustic focusing systems through an environmental reference table and impedance spectroscopy (2018)
    Public Library of Science
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 13 (2018): e0207532, doi:10.1371/journal.pone.0207532.
    Description: Acoustic standing waves can precisely focus flowing particles or cells into tightly positioned streams for interrogation or downstream separations. The efficiency of an acoustic standing wave device is dependent upon operating at a resonance frequency. Small changes in a system’s temperature and sample salinity can shift the device’s resonance condition, leading to poor focusing. Practical implementation of an acoustic standing wave system requires an automated resonance control system to adjust the standing wave frequency in response to environmental changes. Here we have developed a rigorous approach for quantifying the optimal acoustic focusing frequency at any given environmental condition. We have demonstrated our approach across a wide range of temperature and salinity conditions to provide a robust characterization of how the optimal acoustic focusing resonance frequency shifts across these conditions. To generalize these results, two microfluidic bulk acoustic standing wave systems (a steel capillary and an etched silicon wafer) were examined. Models of these temperature and salinity effects suggest that it is the speed of sound within the liquid sample that dominates the resonance frequency shift. Using these results, a simple reference table can be generated to predict the optimal resonance condition as a function of temperature and salinity. Additionally, we show that there is a local impedance minimum associated with the optimal system resonance. The integration of the environmental results for coarse frequency tuning followed by a local impedance characterization for fine frequency adjustments, yields a highly accurate method of resonance control. Such an approach works across a wide range of environmental conditions, is easy to automate, and could have a significant impact across a wide range of microfluidic acoustic standing wave systems.
    Description: This research was supported by grants from the National Institute of General Medical Sciences of the National Institutes of Health under award number R21GM107805 and the NSF under award number (OCE-1130140 and OCE-1131134) to SWG, RJO, and HMS.
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 17
    facet.materialart.
    Unknown
    Regenerative capacity in the lamprey spinal cord is not altered after a repeated transection (2019)
    Public Library of Science
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 14(1), (2019):e0204193, doi: 10.1371/journal.pone.0204193.
    Description: The resilience of regeneration in vertebrates is not very well understood. Yet understanding if tissues can regenerate after repeated insults, and identifying limitations, is important for elucidating the underlying mechanisms of tissue plasticity. This is particularly challenging in tissues, such as the nervous system, which possess a large number of terminally differentiated cells and often exhibit limited regeneration in the first place. However, unlike mammals, which exhibit very limited regeneration of spinal cord tissues, many non-mammalian vertebrates, including lampreys, bony fishes, amphibians, and reptiles, regenerate their spinal cords and functionally recover even after a complete spinal cord transection. It is well established that lampreys undergo full functional recovery of swimming behaviors after a single spinal cord transection, which is accompanied by tissue repair at the lesion site, as well as axon and synapse regeneration. Here we begin to explore the resilience of spinal cord regeneration in lampreys after a second spinal transection (re-transection). We report that by all functional and anatomical measures tested, lampreys regenerate after spinal re-transection just as robustly as after single transections. Recovery of swimming, synapse and cytoskeletal distributions, axon regeneration, and neuronal survival were nearly identical after spinal transection or re-transection. Only minor differences in tissue repair at the lesion site were observed in re-transected spinal cords. Thus, regenerative potential in the lamprey spinal cord is largely unaffected by spinal re-transection, indicating a greater persistent regenerative potential than exists in some other highly regenerative models. These findings establish a new path for uncovering pro-regenerative targets that could be deployed in non-regenerative conditions.
    Description: The authors would like to thank Dr. Cristina Roman-Vendrell and Louie Kerr, Director of the Central Microscopy Facility at the MBL, for technical support. We also thank Dr. Juan Diaz-Quiroz for helpful comments on the manuscript. EG was supported in part by an NSF REU Award (#1659604: Biological Discovery in Woods Hole at the Marine Biological Laboratory).
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 18
    facet.materialart.
    Unknown
    Inbreeding ratio and genetic relationships among strains of the Western clawed frog, Xenopus tropicalis (2015)
    Public Library of Science
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 10 (2015): e0133963, doi: 10.1371/journal.pone.0133963.
    Description: The Western clawed frog, Xenopus tropicalis, is a highly promising model amphibian, especially in developmental and physiological research, and as a tool for understanding disease. It was originally found in the West African rainforest belt, and was introduced to the research community in the 1990s. The major strains thus far known include the Nigerian and Ivory Coast strains. However, due to its short history as an experimental animal, the genetic relationship among the various strains has not yet been clarified, and establishment of inbred strains has not yet been achieved. Since 2003 the Institute for Amphibian Biology (IAB), Hiroshima University has maintained stocks of multiple X. tropicalis strains and conducted consecutive breeding as part of the National BioResource Project. In the present study we investigated the inbreeding ratio and genetic relationship of four inbred strains at IAB, as well as stocks from other institutions, using highly polymorphic microsatellite markers and mitochondrial haplotypes. Our results show successive reduction of heterozygosity in the genome of the IAB inbred strains. The Ivory Coast strains clearly differed from the Nigerian strains genetically, and three subgroups were identified within both the Nigerian and Ivory Coast strains. It is noteworthy that the Ivory Coast strains have an evolutionary divergent genetic background. Our results serve as a guide for the most effective use of X. tropicalis strains, and the long-term maintenance of multiple strains will contribute to further research efforts.
    Description: This work was supported by grants from the Wellcome Trust (101480/Z/13/Z, http://www.wellcome.ac.uk/stellent/group​s/corporatesite/@msh_publishing_group/do​cuments/web_document/wts058331.pdf) and Biotechnology and Biological Sciences Research Council (BB/K019988/1, http://www.bbsrc.ac.uk/pa/grants/AwardDe​tails.aspx?FundingReference=BB/K019988/1) to the European Xenopus Resource Centre. This work was also supported by a Grant-in-Aid for Young Scientists (B) (No. 23710282, http://kaken.nii.ac.jp/d/p/23710282.en.h​tml) to TI from the Ministry of Education, Culture, Sports, Science and Technology, Japan and a Grant-in-Aid for Scientific Research (B) (No. 20510216, http://kaken.nii.ac.jp/d/p/24310173.en.h​tml) to MS from the Ministry of Education, Culture, Sports, Science and Technology, Japan.
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 19
    facet.materialart.
    Unknown
    The influence of age and gender on skin-associated microbial communities in urban and rural human populations (2015)
    Public Library of Science
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One (10): e0141842, doi:10.1371/journal.pone.0141842.
    Description: Differences in the bacterial community structure associated with 7 skin sites in 71 healthy people over five days showed significant correlations with age, gender, physical skin parameters, and whether participants lived in urban or rural locations in the same city. While body site explained the majority of the variance in bacterial community structure, the composition of the skin-associated bacterial communities were predominantly influenced by whether the participants were living in an urban or rural environment, with a significantly greater relative abundance of Trabulsiella in urban populations. Adults maintained greater overall microbial diversity than adolescents or the elderly, while the intragroup variation among the elderly and rural populations was significantly greater. Skin-associated bacterial community structure and composition could predict whether a sample came from an urban or a rural resident ~5x greater than random.
    Description: This work was supported by a grant from Johnson & Johnson (China).
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: text/plain
    Format: application/pdf
    Format: application/vnd.ms-excel
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 20
    facet.materialart.
    Unknown
    The good, the bad, and the tiny : a simple, mechanistic-probabilistic model of virus-nutrient colimitation in microbes (2016)
    Public Library of Science
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 10 (2015): e0143299, doi:10.1371/journal.pone.0143299.
    Description: For phytoplankton and other microbes, nutrient receptors are often the passages through which viruses invade. This presents a bottom-up vs. top-down, co-limitation scenario; how do these would-be-hosts balance minimizing viral susceptibility with maximizing uptake of limiting nutrient(s)? This question has been addressed in the biological literature on evolutionary timescales for populations, but a shorter timescale, mechanistic perspective is lacking, and marine viral literature suggests the strong influence of additional factors, e.g. host size; while the literature on both nutrient uptake and host-virus interactions is expansive, their intersection, of ubiquitous relevance to marine environments, is understudied. I present a simple, mechanistic model from first principles to analyze the effect of this co-limitation scenario on individual growth, which suggests that in environments with high risk of viral invasion or spatial/temporal heterogeneity, an individual host’s growth rate may be optimized with respect to receptor coverage, producing top-down selective pressure on short timescales. The model has general applicability, is suggestive of hypotheses for empirical exploration, and can be extended to theoretical studies of more complex behaviors and systems.
    Description: This work was supported by the Massachusetts Institute of Technology Charles Vest Presidential Fellowship.
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
    Format: text/csv
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 21
    facet.materialart.
    Unknown
    Site-specific variation in gene expression from Symbiodinium spp. associated with offshore and inshore Porites astreoides in the lower Florida Keys is lost with bleaching and disease stress (2017)
    Public Library of Science
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 12 (2017): e0173350, doi:10.1371/journal.pone.0173350.
    Description: Scleractinian coral are experiencing unprecedented rates of mortality due to increases in sea surface temperatures in response to global climate change. Some coral species however, survive high temperature events due to a reduced susceptibility to bleaching. We investigated the relationship between bleaching susceptibility and expression of five metabolically related genes of Symbiodinium spp. from the coral Porites astreoides originating from an inshore and offshore reef in the Florida Keys. The acclimatization potential of Symbiodinium spp. to changing temperature regimes was also measured via a two-year reciprocal transplant between the sites. Offshore coral fragments displayed significantly higher expression in Symbiodinium spp. genes PCNA, SCP2, G3PDH, PCP and psaE than their inshore counterparts (p〈0.05), a pattern consistent with increased bleaching susceptibility in offshore corals. Additionally, gene expression patterns in Symbiodinium spp. from site of origin were conserved throughout the two-year reciprocal transplant, indicating acclimatization did not occur within this multi-season time frame. Further, laboratory experiments were used to investigate the influence of acute high temperature (32°C for eight hours) and disease (lipopolysaccharide of Serratia marcescens) on the five metabolically related symbiont genes from the same offshore and inshore P. astreoides fragments. Gene expression did not differ between reef fragments, or as a consequence of acute exposure to heat or heat and disease, contrasting to results found in the field. Gene expression reported here indicates functional variation in populations of Symbiodinium spp. associated with P. astreoides in the Florida Keys, and is likely a result of localized adaptation. However, gene expression patterns observed in the lab imply that functional variation in zooxanthellae observed under conditions of chronic moderate stress is lost under the acute extreme conditions studied here.
    Description: Funding for this research was provided by Coastal Preservation network (KBS, BHS).
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 22
    facet.materialart.
    Unknown
    Characterization of trace metal content in the developing zebrafish embryo (2017)
    Public Library of Science
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 12 (2017): e0179318, doi: 10.1371/journal.pone.0179318.
    Description: Trace metals are essential for health but toxic when present in excess. The maintenance of trace metals at physiologic levels reflects both import and export by cells and absorption and excretion by organs. The mechanism by which this maintenance is achieved in vertebrate organisms is incompletely understood. To explore this, we chose zebrafish as our model organism, as they are amenable to both pharmacologic and genetic manipulation and comprise an ideal system for genetic screens and toxicological studies. To characterize trace metal content in developing zebrafish, we measured levels of three trace elements, copper, zinc, and manganese, from the oocyte stage to 30 days post-fertilization using inductively coupled plasma mass spectrometry. Our results indicate that metal levels are stable until zebrafish can acquire metals from the environment and imply that the early embryo relies on maternal contribution of metals to the oocyte. We also measured metal levels in bodies and yolks of embryos reared in presence and absence of the copper chelator neocuproine. All three metals exhibited different relative abundances between yolks and bodies of embryos. While neocuproine treatment led to an expected phenotype of copper deficiency, total copper levels were unaffected, indicating that measurement of total metal levels does not equate with measurement of biologically active metal levels. Overall, our data not only can be used in the design and execution of genetic, physiologic, and toxicologic studies but also has implications for the understanding of vertebrate metal homeostasis.
    Description: This work was supported by the National Institutes of Health, R00 DK84122.
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 23
    facet.materialart.
    Unknown
    African baobabs with false inner cavities : the radiocarbon investigation of the Lebombo Eco Trail Baobab (2015)
    Public Library of Science
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 10 (2015): e0117193, doi:10.1371/journal.pone.0117193.
    Description: The article reports the radiocarbon investigation results of the Lebombo Eco Trail tree, a representative African baobab from Mozambique. Several wood samples collected from the large inner cavity and from the outer part of the tree were investigated by AMS radiocarbon dating. According to dating results, the age values of all samples increase from the sampling point with the distance into the wood. For samples collected from the cavity walls, the increase of age values with the distance into the wood (up to a point of maximum age) represents a major anomaly. The only realistic explanation for this anomaly is that such inner cavities are, in fact, natural empty spaces between several fused stems disposed in a ring-shaped structure. We named them false cavities. Several important differences between normal cavities and false cavities are presented. Eventually, we dated other African baobabs with false inner cavities. We found that this new architecture enables baobabs to reach large sizes and old ages. The radiocarbon date of the oldest sample was 1425 ± 24 BP, which corresponds to a calibrated age of 1355 ± 15 yr. The dating results also show that the Lebombo baobab consists of five fused stems, with ages between 900 and 1400 years; these five stems build the complete ring. The ring and the false cavity closed 800–900 years ago. The results also indicate that the stems stopped growing toward the false cavity over the past 500 years.
    Description: The research was fully funded by the Romanian Ministry of National Education CNCS-UEFISCDI under grant PN-II-ID-PCE-2013-76.
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 24
    facet.materialart.
    Unknown
    An integrated assessment model for helping the United States sea scallop (Placopecten magellanicus) fishery plan ahead for ocean acidification and warming (2015)
    Public Library of Science
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This is an open access article, free of all copyright. The definitive version was published in PLoS One 10 (2015): e0124145, doi:10.1371/journal.pone.0124145.
    Description: Ocean acidification, the progressive change in ocean chemistry caused by uptake of atmospheric CO2, is likely to affect some marine resources negatively, including shellfish. The Atlantic sea scallop (Placopecten magellanicus) supports one of the most economically important single-species commercial fisheries in the United States. Careful management appears to be the most powerful short-term factor affecting scallop populations, but in the coming decades scallops will be increasingly influenced by global environmental changes such as ocean warming and ocean acidification. In this paper, we describe an integrated assessment model (IAM) that numerically simulates oceanographic, population dynamic, and socioeconomic relationships for the U.S. commercial sea scallop fishery. Our primary goal is to enrich resource management deliberations by offering both short- and long-term insight into the system and generating detailed policy-relevant information about the relative effects of ocean acidification, temperature rise, fishing pressure, and socioeconomic factors on the fishery using a simplified model system. Starting with relationships and data used now for sea scallop fishery management, the model adds socioeconomic decision making based on static economic theory and includes ocean biogeochemical change resulting from CO2 emissions. The model skillfully reproduces scallop population dynamics, market dynamics, and seawater carbonate chemistry since 2000. It indicates sea scallop harvests could decline substantially by 2050 under RCP 8.5 CO2 emissions and current harvest rules, assuming that ocean acidification affects P. magellanicus by decreasing recruitment and slowing growth, and that ocean warming increases growth. Future work will explore different economic and management scenarios and test how potential impacts of ocean acidification on other scallop biological parameters may influence the social-ecological system. Future empirical work on the effect of ocean acidification on sea scallops is also needed.
    Description: Cooley, Rheuban, and Doney were supported by NOAA Grant NA12NOS4780145 (www.noaa.gov) and the Center for Climate and Energy Decision Making (CEDM, NSF SES-0949710) (www.nsf.gov). Luu was supported by a WHOI Summer Student Fellowship (www.whoi.edu).
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 25
    facet.materialart.
    Unknown
    Destructive changes in the neuronal structure of the FVB/N mouse retina (2015)
    Public Library of Science
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 10 (2015): e0129719, doi: 10.1371/journal.pone.0129719.
    Description: We applied a series of selective antibodies for labeling the various cell types in the mammalian retina. These were used to identify the progressive loss of neurons in the FVB/N mouse, a model of early onset retinal degeneration produced by a mutation in the pde6b gene. The immunocytochemical studies, together with electroretinogram (ERG) recordings, enabled us to examine the time course of the degenerative changes that extended from the photoreceptors to the ganglion cells at the proximal end of the retina. Our study indicates that photoreceptors in FVB/N undergo a rapid degeneration within three postnatal weeks, and that there is a concomitant loss of retinal neurons in the inner nuclear layer. Although the loss of rods was detected at an earlier age during which time M- and S-opsin molecules were translocated to the cone nuclei; by 6 months all cones had also degenerated. Neuronal remodeling was also seen in the second-order neurons with horizontal cells sprouting processes proximally and dendritic retraction in rod-driven bipolar cells. Interestingly, the morphology of cone-driven bipolar cells were affected less by the disease process. The cellular structure of inner retinal neurons, i.e., ChAT amacrine cells, ganglion cells, and melanopsin-positive ganglion cells did not exhibit any gross changes of cell densities and appeared to be relatively unaffected by the massive photoreceptor degeneration in the distal retina. However, Muller cell processes began to express GFAP at their endfeet at p14, and it climbed progressively to the cell’s distal ends by 6 months. Our study indicates that FVB/N mouse provides a useful model with which to assess possible intervention strategies to arrest photoreceptor death in related diseases.
    Description: This study was supported by grants from the National Science Foundation (NSF, IOS-1021646, WS) and the National Eye Institute (NEI, EY 14161, WS).
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 26
    facet.materialart.
    Unknown
    AMS radiocarbon dating of large za baobabs (Adansonia za) of Madagascar (2016)
    Public Library of Science
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 11 (2016): e0146977, doi:10.1371/journal.pone.0146977 .
    Description: The article reports the radiocarbon investigation of Anzapalivoro, the largest za baobab (Adansonia za) specimen of Madagascar and of another za, namely the Big cistern baobab. Several wood samples collected from the large inner cavity and from the outer part/exterior of the tree were investigated by AMS (accelerator mass spectrometry) radiocarbon dating. For samples collected from the cavity walls, the age values increase with the distance into the wood up to a point of maximum age, after which the values decrease toward the outer part. This anomaly of age sequences indicates that the inner cavity of Anzapalivoro is a false cavity, practically an empty space between several fused stems disposed in a ring-shaped structure. The radiocarbon date of the oldest sample was 780 ± 30 bp, which corresponds to a calibrated age of around 735 yr. Dating results indicate that Anzapalivoro has a closed ring-shaped structure, which consists of 5 fused stems that close a false cavity. The oldest part of the biggest za baobab has a calculated age of 900 years. We also disclose results of the investigation of a second za baobab, the Big cistern baobab, which was hollowed out for water storage. This specimen, which consists of 4 fused stems, was found to be around 260 years old.
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 27
    facet.materialart.
    Unknown
    Biochemical mechanisms for geographical adaptations to novel toxin exposures in butterflyfish (2016)
    Public Library of Science
    Details
    Publication Date: 2022-05-25
    Description: This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The definitive version was published in PLoS One 11 (2016): e0154208, doi: 10.1371/journal.pone.0154208
    Description: Some species of butterflyfish have had preyed upon corals for millions of years, yet the mechanism of butterflyfish specialized coral feeding strategy remains poorly understood. Certain butterflyfish have the ability to feed on allelochemically rich soft corals, e.g. Sinularia maxima. Cytochrome P450 (CYP) is the predominant enzyme system responsible for the detoxification of dietary allelochemicals. CYP2-like and CYP3A-like content have been associated with butterflyfish that preferentially consumes allelochemically rich soft corals. To investigate the role of butterflyfish CYP2 and CYP3A enzymes in dietary preference, we conducted oral feeding experiments using homogenates of S. maxima and a toxin isolated from the coral in four species of butterflyfish with different feeding strategies. After oral exposure to the S. maxima toxin 5-episinulaptolide (5ESL), which is not normally encountered in the Hawaiian butterflyfish diet, an endemic specialist, Chaetodon multicinctus experienced 100% mortality compared to a generalist, Chaetodon auriga, which had significantly more (3–6 fold higher) CYP3A-like basal content and catalytic activity. The specialist, Chaetodon unimaculatus, which preferentially feed on S. maxima in Guam, but not in Hawaii, had 100% survival, a significant induction of 8–12 fold CYP3A-like content, and an increased ability (2-fold) to metabolize 5ESL over other species. Computer modeling data of CYP3A4 with 5ESL were consistent with microsomal transformation of 5ESL to a C15-16 epoxide from livers of C. unimaculatus. Epoxide formation correlated with CYP3A-like content, catalytic activity, induction, and NADPH-dependent metabolism of 5ESL. These results suggest a potentially important role for the CYP3A family in butterflyfish-coral diet selection through allelochemical detoxification.
    Description: This work received support from the following sources: Resource Allocation Program of the Agricultural Research Station for UCR to DS; Summer funding by Hilda and George Liebig Environmental Sciences Summer Fellowship and travel grant Albert March Environmental Sciences Scholarship from the University of California, Riverside; and the Chemistry and DMPK CORE of COBRE, P20GM104932 from the National Institute of General Medical Sciences (NIGMS), a component of the National Institutes of Health (NIH) supported the chemistry studies.
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 28
    facet.materialart.
    Unknown
    Smartphone-based distributed data collection enables rapid assessment of shorebird habitat suitability (2016)
    Public Library of Science
    Details
    Publication Date: 2022-05-25
    Description: This is an open access article, free of all copyright. The definitive version was published in PLoS ONE 11 (2016): e0164979, doi: 10.1371/journal.pone.0164979.
    Description: Understanding and managing dynamic coastal landscapes for beach-dependent species requires biological and geological data across the range of relevant environments and habitats. It is difficult to acquire such information; data often have limited focus due to resource constraints, are collected by non-specialists, or lack observational uniformity. We developed an open-source smartphone application called iPlover that addresses these difficulties in collecting biogeomorphic information at piping plover (Charadrius melodus) nest sites on coastal beaches. This paper describes iPlover development and evaluates data quality and utility following two years of collection (n = 1799 data points over 1500 km of coast between Maine and North Carolina, USA). We found strong agreement between field user and expert assessments and high model skill when data were used for habitat suitability prediction. Methods used here to develop and deploy a distributed data collection system have broad applicability to interdisciplinary environmental monitoring and modeling.
    Description: This work was supported by the North Atlantic Landscape Conservation Cooperative through the U.S. Department of the Interior Hurricane Sandy recovery program under the Disaster Relief Appropriations Act of 2013, and the U.S. Geological Survey Coastal and Marine Geology Program.
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 29
    facet.materialart.
    Unknown
    Strength in numbers : collaborative science for new experimental model systems (2018)
    Public Library of Science
    Details
    Publication Date: 2022-05-25
    Description: The work is made available under the Creative Commons CCO public domain dedication.. The definitive version was published in PLoS Biology 16 (2018): e2006333, doi:10.1371/journal.pbio.2006333.
    Description: Our current understanding of biology is heavily based on a small number of genetically tractable model organisms. Most eukaryotic phyla lack such experimental models, and this limits our ability to explore the molecular mechanisms that ultimately define their biology, ecology, and diversity. In particular, marine protists suffer from a paucity of model organisms despite playing critical roles in global nutrient cycles, food webs, and climate. To address this deficit, an initiative was launched in 2015 to foster the development of ecologically and taxonomically diverse marine protist genetic models. The development of new models faces many barriers, some technical and others institutional, and this often discourages the risky, long-term effort that may be required. To lower these barriers and tackle the complexity of this effort, a highly collaborative community-based approach was taken. Herein, we describe this approach, the advances achieved, and the lessons learned by participants in this novel community-based model for research.
    Description: The research efforts, connections, and collaborations described in this paper and protocols.io (https://www.protocols.io/) were supported by the Gordon and Betty Moore Foundation’s Marine Microbiology Initiative.
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 30
    facet.materialart.
    Unknown
    Multi-use of the sea: A wide array of opportunities from site-specific cases across Europe (2019)
    Public Library of Science
    In:  EPIC3PLOS ONE, Public Library of Science, 14(4), pp. 1-36
    Details
    Publication Date: 2020-02-27
    Description: The concept of multi-use of the sea has gained popularity in recent years as a result of ocean space (coastal areas and regions with relatively small sea space in particular) becoming increasingly crowded due to the development of the maritime economy. Competing claims for space can be a source of conflict, however this may also lead to mutual benefits for different users when sustainable combinations are sought. Despite increasing European-wide efforts, on-the-ground knowledge and practice of multi-use are still limited. Therefore, with the aim of investigating opportunities for multi-use development in the European seas, 10 case studies were selected, involving different site-specific contexts. This study analyses the characteristics and development potential for ocean multi-use, integrating results from desk analysis and stakeholder perceptions from different sectors in each of the case study locations. Similarities and differences between various combinations of sea uses are also identified. The results show a high heterogeneity of multi-use opportunities between case studies, with a range of combinations identified. The investigated combinations of maritime uses share an overall balance between factors promoting (drivers) and hindering (barriers) multi-use development. Based on stakeholder opinions, expected benefits (added values) of multi-use implementation outweigh potential negative impacts. Management actions are also proposed to further exploit multi-use potential at a local, regional (sub-national) and national levels.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev , info:eu-repo/semantics/article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 31
    facet.materialart.
    Unknown
    Reef-fidelity and migration of tiger sharks, Galeocerdo cuvier, across the Coral Sea (2015)
    Public Library of Science
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e83249, doi:10.1371/journal.pone.0083249.
    Description: Knowledge of the habitat use and migration patterns of large sharks is important for assessing the effectiveness of large predator Marine Protected Areas (MPAs), vulnerability to fisheries and environmental influences, and management of shark–human interactions. Here we compare movement, reef-fidelity, and ocean migration for tiger sharks, Galeocerdo cuvier, across the Coral Sea, with an emphasis on New Caledonia. Thirty-three tiger sharks (1.54 to 3.9 m total length) were tagged with passive acoustic transmitters and their localised movements monitored on receiver arrays in New Caledonia, the Chesterfield and Lord Howe Islands in the Coral Sea, and the east coast of Queensland, Australia. Satellite tags were also used to determine habitat use and movements among habitats across the Coral Sea. Sub-adults and one male adult tiger shark displayed year-round residency in the Chesterfields with two females tagged in the Chesterfields and detected on the Great Barrier Reef, Australia, after 591 and 842 days respectively. In coastal barrier reefs, tiger sharks were transient at acoustic arrays and each individual demonstrated a unique pattern of occurrence. From 2009 to 2013, fourteen sharks with satellite and acoustic tags undertook wide-ranging movements up to 1114 km across the Coral Sea with eight detected back on acoustic arrays up to 405 days after being tagged. Tiger sharks dove 1136 m and utilised three-dimensional activity spaces averaged at 2360 km3. The Chesterfield Islands appear to be important habitat for sub-adults and adult male tiger sharks. Management strategies need to consider the wide-ranging movements of large (sub-adult and adult) male and female tiger sharks at the individual level, whereas fidelity to specific coastal reefs may be consistent across groups of individuals. Coastal barrier reef MPAs, however, only afford brief protection for large tiger sharks, therefore determining the importance of other oceanic Coral Sea reefs should be a priority for future research.
    Description: Funding was provided by the the Agence Francaise de Développement (http://www.afd.fr), French Pacific Fund, the CRISP program (www.crisponline.info) and QLD Fisheries.
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
    Format: video/mp4
    Format: text/plain
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 32
    facet.materialart.
    Unknown
    Chemical composition and potential environmental impacts of water-soluble polar crude oil components inferred from ESI FT-ICR MS (2015)
    Public Library of Science
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 10 (2015): e0136376, doi:10.1371/journal.pone.0136376.
    Description: Polar petroleum components enter marine environments through oil spills and natural seepages each year. Lately, they are receiving increased attention due to their potential toxicity to marine organisms and persistence in the environment. We conducted a laboratory experiment and employed state-of-the-art Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) to characterize the polar petroleum components within two operationally-defined seawater fractions: the water-soluble fraction (WSF), which includes only water-soluble molecules, and the water-accommodated fraction (WAF), which includes WSF and microscopic oil droplets. Our results show that compounds with higher heteroatom (N, S, O) to carbon ratios (NSO:C) than the parent oil were selectively partitioned into seawater in both fractions, reflecting the influence of polarity on aqueous solubility. WAF and WSF were compositionally distinct, with unique distributions of compounds across a range of hydrophobicity. These compositional differences will likely result in disparate impacts on environmental health and organismal toxicity, and thus highlight the need to distinguish between these often-interchangeable terminologies in toxicology studies. We use an empirical model to estimate hydrophobicity character for individual molecules within these complex mixtures and provide an estimate of the potential environmental impacts of different crude oil components.
    Description: This study is funded by the Gulf of Mexico Research Initiative (GOMRI) Project # 161684 to Dr. Elizabeth B. Kujawinski.
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: text/plain
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 33
    facet.materialart.
    Unknown
    An unexpected diversity of photoreceptor classes in the longfin squid, Doryteuthis pealeii (2015)
    Public Library of Science
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 10 (2015): e0135381, doi:10.1371/journal.pone.0135381.
    Description: Cephalopods are famous for their ability to change color and pattern rapidly for signaling and camouflage. They have keen eyes and remarkable vision, made possible by photoreceptors in their retinas. External to the eyes, photoreceptors also exist in parolfactory vesicles and some light organs, where they function using a rhodopsin protein that is identical to that expressed in the retina. Furthermore, dermal chromatophore organs contain rhodopsin and other components of phototransduction (including retinochrome, a photoisomerase first found in the retina), suggesting that they are photoreceptive. In this study, we used a modified whole-mount immunohistochemical technique to explore rhodopsin and retinochrome expression in a number of tissues and organs in the longfin squid, Doryteuthis pealeii. We found that fin central muscles, hair cells (epithelial primary sensory neurons), arm axial ganglia, and sucker peduncle nerves all express rhodopsin and retinochrome proteins. Our findings indicate that these animals possess an unexpected diversity of extraocular photoreceptors and suggest that extraocular photoreception using visual opsins and visual phototransduction machinery is far more widespread throughout cephalopod tissues than previously recognized.
    Description: This research was supported by the Office of Naval Research Basic Research Challenge grant number N00014-10-0989 to TWC and RTH and a Biotechnology and Biological Sciences Research Council (BBSRC) David Phillips Fellowship BB/L024667/1 to TJW. The authors gratefully acknowledge support from the Air Force Office of Scientific Research via grants numbered FA9550-09-0346 to RTH. and FA9550-12-1-0321 to TWC.
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
    Format: text/plain
    Format: image/tiff
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 34
    facet.materialart.
    Unknown
    Analysis of lung microbiota in bronchoalveolar lavage, protected brush and sputum samples from subjects with mild-to-moderate cystic fibrosis Lung Disease (2016)
    Public Library of Science
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS 11 (2016): e0149998, doi:10.1371/journal.pone.0149998.
    Description: Individuals with cystic fibrosis (CF) often acquire chronic lung infections that lead to irreversible damage. We sought to examine regional variation in the microbial communities in the lungs of individuals with mild-to-moderate CF lung disease, to examine the relationship between the local microbiota and local damage, and to determine the relationships between microbiota in samples taken directly from the lung and the microbiota in spontaneously expectorated sputum. In this initial study, nine stable, adult CF patients with an FEV1〉50% underwent regional sampling of different lobes of the right lung by bronchoalveolar lavage (BAL) and protected brush (PB) sampling of mucus plugs. Sputum samples were obtained from six of the nine subjects immediately prior to the procedure. Microbial community analysis was performed on DNA extracted from these samples and the extent of damage in each lobe was quantified from a recent CT scan. The extent of damage observed in regions of the right lung did not correlate with specific microbial genera, levels of community diversity or composition, or bacterial genome copies per ml of BAL fluid. In all subjects, BAL fluid from different regions of the lung contained similar microbial communities. In eight out of nine subjects, PB samples from different regions of the lung were also similar in microbial community composition, and were similar to microbial communities in BAL fluid from the same lobe. Microbial communities in PB samples were more diverse than those in BAL samples, suggesting enrichment of some taxa in mucus plugs. To our knowledge, this study is the first to examine the microbiota in different regions of the CF lung in clinically stable individuals with mild-to-moderate CF-related lung disease.
    Description: Support from the Cystic Fibrosis Foundation Research Development Program (STANTO07R0) as a pilot grant to DAH and AA. Research reported in this publication was also supported by grants from the National Institutes of Health to DAH (R01 AI091702 to DAH) and the American Asthma Foundation Scholars Award and CFFT-ASHARE15A0 and R01HL122372 to AA and R01 HL074175 (BAS). The Dartmouth Lung Biology Center and CF Translational Research Core was supported by an Institutional Development Award (IDeA) from the National Institute of General Medical Sciences of the National Institutes of Health under grant number P30GM106394 and by the CFF RDP (CFRDP STANTO11R0).
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 35
    facet.materialart.
    Unknown
    Abundance and distribution of sperm whales in the Canary Islands : can sperm whales in the archipelago sustain the current level of ship-strike mortalities? (2016)
    Public Library of Science
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS 11 (2016): e0150660, doi:10.1371/journal.pone.0150660.
    Description: Sperm whales are present in the Canary Islands year-round, suggesting that the archipelago is an important area for this species in the North Atlantic. However, the area experiences one of the highest reported rates of sperm whale ship-strike in the world. Here we investigate if the number of sperm whales found in the archipelago can sustain the current rate of ship-strike mortality. The results of this study may also have implications for offshore areas where concentrations of sperm whales may coincide with high densities of ship traffic, but where ship-strikes may be undocumented. The absolute abundance of sperm whales in an area of 52933 km2, covering the territorial waters of the Canary Islands, was estimated from 2668 km of acoustic line-transect survey using Distance sampling analysis. Data on sperm whale diving and acoustic behaviour, obtained from bio-logging, were used to calculate g(0) = 0.92, this is less than one because of occasional extended periods when whales do not echolocate. This resulted in an absolute abundance estimate of 224 sperm whales (95% log-normal CI 120–418) within the survey area. The recruitment capability of this number of whales, some 2.5 whales per year, is likely to be exceeded by the current ship-strike mortality rate. Furthermore, we found areas of higher whale density within the archipelago, many coincident with those previously described, suggesting that these are important habitats for females and immature animals inhabiting the archipelago. Some of these areas are crossed by active shipping lanes increasing the risk of ship-strikes. Given the philopatry in female sperm whales, replacement of impacted whales might be limited. Therefore, the application of mitigation measures to reduce the ship-strike mortality rate seems essential for the conservation of sperm whales in the Canary Islands.
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 36
    facet.materialart.
    Unknown
    Cisplatin resistant spheroids model clinically relevant survival mechanisms in ovarian tumors (2016)
    Public Library of Science
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS 11 (2016): e0151089, doi: 10.1371/journal.pone.0151089 .
    Description: The majority of ovarian tumors eventually recur in a drug resistant form. Using cisplatin sensitive and resistant cell lines assembled into 3D spheroids we profiled gene expression and identified candidate mechanisms and biological pathways associated with cisplatin resistance. OVCAR-8 human ovarian carcinoma cells were exposed to sub-lethal concentrations of cisplatin to create a matched cisplatin-resistant cell line, OVCAR-8R. Genome-wide gene expression profiling of sensitive and resistant ovarian cancer spheroids identified 3,331 significantly differentially expressed probesets coding for 3,139 distinct protein-coding genes (Fc 〉2, FDR 〈 0.05) (S2 Table). Despite significant expression changes in some transporters including MDR1, cisplatin resistance was not associated with differences in intracellular cisplatin concentration. Cisplatin resistant cells were significantly enriched for a mesenchymal gene expression signature. OVCAR-8R resistance derived gene sets were significantly more biased to patients with shorter survival. From the most differentially expressed genes, we derived a 17-gene expression signature that identifies ovarian cancer patients with shorter overall survival in three independent datasets. We propose that the use of cisplatin resistant cell lines in 3D spheroid models is a viable approach to gain insight into resistance mechanisms relevant to ovarian tumors in patients. Our data support the emerging concept that ovarian cancers can acquire drug resistance through an epithelial-to-mesenchymal transition.
    Description: This work was funded by the NIH NCRR supplement grant P41 RR001395-27S1 (J.W.H.), NSF DBI-1005378 “REU Site: Biological Discovery in Woods Hole”, faculty startup funds from the Office of Research at Oklahoma State University (W.C.), and the Mary Kay Foundation (A.S.B.).
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 37
    facet.materialart.
    Unknown
    Multi-method assessment of whale shark (Rhincodon typus) residency, distribution, and dispersal behavior at an aggregation site in the Red Sea (2019)
    Public Library of Science
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Cochran, J. E. M., Braun, C. D., Cagua, E. F., Campbell, M. F., Hardenstine, R. S., Kattan, A., Priest, M. A., Sinclair-Taylor, T. H., Skomal, G. B., Sultan, S., Sun, L., Thorrold, S. R., & Berumen, M. L. Multi-method assessment of whale shark (Rhincodon typus) residency, distribution, and dispersal behavior at an aggregation site in the Red Sea. Plos One, 14(9), (2019): e0222285, doi:10.1371/journal.pone.0222285.
    Description: Whale sharks (Rhincodon typus) are typically dispersed throughout their circumtropical range, but the species is also known to aggregate in specific coastal areas. Accurate site descriptions associated with these aggregations are essential for the conservation of R. typus, an Endangered species. Although aggregations have become valuable hubs for research, most site descriptions rely heavily on sightings data. In the present study, visual census, passive acoustic monitoring, and long range satellite telemetry were combined to track the movements of R. typus from Shib Habil, a reef-associated aggregation site in the Red Sea. An array of 63 receiver stations was used to record the presence of 84 acoustically tagged sharks (35 females, 37 males, 12 undetermined) from April 2010 to May 2016. Over the same period, identification photos were taken for 76 of these tagged individuals and 38 were fitted with satellite transmitters. In total of 37,461 acoustic detections, 210 visual encounters, and 33 satellite tracks were analyzed to describe the sharks’ movement ecology. The results demonstrate that the aggregation is seasonal, mostly concentrated on the exposed side of Shib Habil, and seems to attract sharks of both sexes in roughly equal numbers. The combined methodologies also tracked 15 interannual homing-migrations, demonstrating that many sharks leave the area before returning in later years. When compared to acoustic studies from other aggregations, these results demonstrate that R. typus exhibits diverse, site-specific ecologies across its range. Sightings-independent data from acoustic telemetry and other sources are an effective means of validating more common visual surveys.
    Description: Financial support was provided in part by KAUST baseline research funds (to MLB), KAUST award nos. USA00002 and KSA 00011 (to SRT), and the U.S. National Science Foundation (OCE 0825148 to SRT and GBS).
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 38
    facet.materialart.
    Unknown
    Multiplexed spectral imaging of 120 different fluorescent labels (2016)
    Public Library of Science
    Details
    Publication Date: 2022-05-26
    Description: This article is distributed under the terms of the Creative Commons public domain dedication. The definitive version was published in PLoS One 11 (2016): e0158495, doi:10.1371/journal.pone.0158495.
    Description: The number of fluorescent labels that can unambiguously be distinguished in a single image when acquired through band pass filters is severely limited by the spectral overlap of available fluorophores. The recent development of spectral microscopy and the application of linear unmixing algorithms to spectrally recorded image data have allowed simultaneous imaging of fluorophores with highly overlapping spectra. However, the number of distinguishable fluorophores is still limited by the unavoidable decrease in signal to noise ratio when fluorescence signals are fractionated over multiple wavelength bins. Here we present a spectral image analysis algorithm to greatly expand the number of distinguishable objects labeled with binary combinations of fluorophores. Our algorithm utilizes a priori knowledge about labeled specimens and imposes a binary label constraint on the unmixing solution. We have applied our labeling and analysis strategy to identify microbes labeled by fluorescence in situ hybridization and here demonstrate the ability to distinguish 120 differently labeled microbes in a single image.
    Description: This work was supported by Grant 2007-3- 13 from the Alfred P. Sloan Foundation (to GGB), National Institutes of Health Grant 1RC1-DE020630 from the National Institute of Dental and Craniofacial Research (NIDCR) (to GGB) and by National Institutes of Health Fellowship 1F31-DE019576 from NIDCR (to AMV).
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 39
    facet.materialart.
    Unknown
    Influence of acidic pH on hydrogen and acetate production by an electrosynthetic microbiome (2015)
    Public Library of Science
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 9 (2014): e109935, doi:10.1371/journal.pone.0109935.
    Description: Production of hydrogen and organic compounds by an electrosynthetic microbiome using electrodes and carbon dioxide as sole electron donor and carbon source, respectively, was examined after exposure to acidic pH (~5). Hydrogen production by biocathodes poised at −600 mV vs. SHE increased〉100-fold and acetate production ceased at acidic pH, but ~5–15 mM (catholyte volume)/day acetate and〉1,000 mM/day hydrogen were attained at pH ~6.5 following repeated exposure to acidic pH. Cyclic voltammetry revealed a 250 mV decrease in hydrogen overpotential and a maximum current density of 12.2 mA/cm2 at −765 mV (0.065 mA/cm2 sterile control at −800 mV) by the Acetobacterium-dominated community. Supplying −800 mV to the microbiome after repeated exposure to acidic pH resulted in up to 2.6 kg/m3/day hydrogen (≈2.6 gallons gasoline equivalent), 0.7 kg/m3/day formate, and 3.1 kg/m3/day acetate ( = 4.7 kg CO2 captured).
    Description: This research was supported by a grant from the Department of Energy, Advanced Projects Research Agency – Energy (DE-AR0000089). CWM was supported with a Director's Postdoctoral Fellowship from Argonne National Laboratory.
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: video/quicktime
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 40
    facet.materialart.
    Unknown
    Searching for the oldest baobab of Madagascar : radiocarbon investigation of large Adansonia rubrostipa trees (2015)
    Public Library of Science
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 10 (2015): e0121170, doi:10.1371/journal.pone.0121170.
    Description: We extended our research on the architecture, growth and age of trees belonging to the genus Adansonia, by starting to investigate large individuals of the most widespread Malagasy species. Our research also intends to identify the oldest baobabs of Madagascar. Here we present results of the radiocarbon investigation of the two most representative Adansonia rubrostipa (fony baobab) specimens, which are located in south-western Madagascar, in the Tsimanampetsotse National Park. We found that the fony baobab called “Grandmother” consists of 3 perfectly fused stems of different ages. The radiocarbon date of the oldest sample was found to be 1136 ± 16 BP. We estimated that the oldest part of this tree, which is mainly hollow, has an age close to 1,600 yr. This value is comparable to the age of the oldest Adansonia digitata (African baobab) specimens. By its age, the Grandmother is a major candidate for the oldest baobab of Madagascar. The second investigated specimen, called the “polygamous baobab”, consists of 6 partially fused stems of different ages. According to dating results, this fony baobab is 1,000 yr old. This research is the first investigation of the structure and age of Malagasy baobabs.
    Description: The research was fully funded by the Romanian Ministry of National Education CNCS-UEFISCDI under grant PN-II-ID-PCE-2013-76 (URL: http://uefiscdi.gov.ro/).
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 41
    facet.materialart.
    Unknown
    Methanol production by a broad phylogenetic array of marine phytoplankton (2016)
    Public Library of Science
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS 11 (2016): e0150820, doi:10.1371/journal.pone.0150820.
    Description: Methanol is a major volatile organic compound on Earth and serves as an important carbon and energy substrate for abundant methylotrophic microbes. Previous geochemical surveys coupled with predictive models suggest that the marine contributions are exceedingly large, rivaling terrestrial sources. Although well studied in terrestrial ecosystems, methanol sources are poorly understood in the marine environment and warrant further investigation. To this end, we adapted a Purge and Trap Gas Chromatography/Mass Spectrometry (P&T-GC/MS) method which allowed reliable measurements of methanol in seawater and marine phytoplankton cultures with a method detection limit of 120 nanomolar. All phytoplankton tested (cyanobacteria: Synechococcus spp. 8102 and 8103, Trichodesmium erythraeum, and Prochlorococcus marinus), and Eukarya (heterokont diatom: Phaeodactylum tricornutum, coccolithophore: Emiliania huxleyi, cryptophyte: Rhodomonas salina, and non-diatom heterokont: Nannochloropsis oculata) produced methanol, ranging from 0.8–13.7 micromolar in culture and methanol per total cellular carbon were measured in the ranges of 0.09–0.3%. Phytoplankton culture time-course measurements displayed a punctuated production pattern with maxima near early stationary phase. Stabile isotope labeled bicarbonate incorporation experiments confirmed that methanol was produced from phytoplankton biomass. Overall, our findings suggest that phytoplankton are a major source of methanol in the upper water column of the world’s oceans.
    Description: This project was solely supported by a grant to TJM from the National Science Foundation (Award# CHE-OCE 1131415).
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 42
    facet.materialart.
    Unknown
    Interspecific hybridization in pilot whales and asymmetric genetic introgression in northern Globicephala melas under the scenario of global warming (2016)
    Public Library of Science
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 11 (2016): e0160080, doi: 10.1371/journal.pone.0160080 .
    Description: Pilot whales are two cetacean species (Globicephala melas and G. macrorhynchus) whose distributions are correlated with water temperature and partially overlap in some areas like the North Atlantic Ocean. In the context of global warming, distribution range shifts are expected to occur in species affected by temperature. Consequently, a northward displacement of the tropical pilot whale G. macrorynchus is expected, eventually leading to increased secondary contact areas and opportunities for interspecific hybridization. Here, we describe genetic evidences of recurrent hybridization between pilot whales in northeast Atlantic Ocean. Based on mitochondrial DNA sequences and microsatellite loci, asymmetric introgression of G. macrorhynchus genes into G. melas was observed. For the latter species, a significant correlation was found between historical population growth rate estimates and paleotemperature oscillations. Introgressive hybridization, current temperature increases and lower genetic variation in G. melas suggest that this species could be at risk in its northern range. Under increasing environmental and human-mediated stressors in the North Atlantic Ocean, it seems recommendable to develop a conservation program for G. melas.
    Description: LM had a PCTI Grant from the Asturias Regional Government, referenced BP 10-004. MAS was supported by a 2013 FCT Investigator contract through POPH, QREN European Social Fund and the Portuguese Ministry for Science and Education. This study was also supported by a grant from the Principality of Asturias (reference: GRUPIN-2014-093).
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 43
    facet.materialart.
    Unknown
    Using a Bayesian network to understand the importance of coastal storms and undeveloped landscapes for the creation and maintenance of early successional habitat (2019)
    Public Library of Science
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Zeigler, S. L., Gutierrez, B. T., Sturdivant, E. J., Catlin, D. H., Fraser, J. D., Hecht, A., Karpanty, S. M., Plant, N. G., & Thieler, E. R. Using a Bayesian network to understand the importance of coastal storms and undeveloped landscapes for the creation and maintenance of early successional habitat. Plos One, 14(7), (2019): e0209986, doi:10.1371/journal.pone.0209986.
    Description: Coastal storms have consequences for human lives and infrastructure but also create important early successional habitats for myriad species. For example, storm-induced overwash creates nesting habitat for shorebirds like piping plovers (Charadrius melodus). We examined how piping plover habitat extent and location changed on barrier islands in New York, New Jersey, and Virginia after Hurricane Sandy made landfall following the 2012 breeding season. We modeled nesting habitat using a nest presence/absence dataset that included characterizations of coastal morphology and vegetation. Using a Bayesian network, we predicted nesting habitat for each study site for the years 2010/2011, 2012, and 2014/2015 based on remotely sensed spatial datasets (e.g., lidar, orthophotos). We found that Hurricane Sandy increased piping plover habitat by 9 to 300% at 4 of 5 study sites but that one site saw a decrease in habitat by 27%. The amount, location, and longevity of new habitat appeared to be influenced by the level of human development at each site. At three of the five sites, the amount of habitat created and the time new habitat persisted were inversely related to the amount of development. Furthermore, the proportion of new habitat created in high-quality overwash was inversely related to the level of development on study areas, from 17% of all new habitat in overwash at one of the most densely developed sites to 80% of all new habitat at an undeveloped site. We also show that piping plovers exploited new habitat after the storm, with 14–57% of all nests located in newly created habitat in the 2013 breeding season. Our results quantify the importance of storms in creating and maintaining coastal habitats for beach-nesting species like piping plovers, and these results suggest a negative correlation between human development and beneficial ecological impacts of these natural disturbances.
    Description: Funding for this work was provided through a U.S. Geological Survey Mendenhall Post-Doctoral Fellowship awarded to S. Zeigler, with funding for this fellowship made through a grant to E.R. Thieler from the North Atlantic Landscape Conservation Cooperative. Funders did not play a role in study design, data collection or analysis, decision to publish, or preparation of the manuscript.
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 44
    facet.materialart.
    Unknown
    Differential cellular responses associated with oxidative stress and cell fate decision under nitrate and phosphate limitations in Thalassiosira pseudonana : comparative proteomics (2017)
    Public Library of Science
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 12 (2017): e0184849, doi:10.1371/journal.pone.0184849.
    Description: Diatoms are important components of marine ecosystems and contribute greatly to the world's primary production. Despite their important roles in ecosystems, the molecular basis of how diatoms cope with oxidative stress caused by nutrient fluctuations remains largely unknown. Here, an isobaric tags for relative and absolute quantitation (iTRAQ) proteomic method was coupled with a series of physiological and biochemical techniques to explore oxidative stress- and cell fate decision-related cellular and metabolic responses of the diatom Thalassiosira pseudonana to nitrate (N) and inorganic phosphate (P) stresses. A total of 1151 proteins were detected; 122 and 56 were significantly differentially expressed from control under N- and P-limited conditions, respectively. In N-limited cells, responsive proteins were related to reactive oxygen species (ROS) accumulation, oxidative stress responses and cell death, corresponding to a significant decrease in photosynthetic efficiency, marked intracellular ROS accumulation, and caspase-mediated programmed cell death activation. None of these responses were identified in P-limited cells; however, a significant up-regulation of alkaline phosphatase proteins was observed, which could be the major contributor for P-limited cells to cope with ambient P deficiency. These findings demonstrate that fundamentally different metabolic responses and cellular regulations are employed by the diatom in response to different nutrient stresses and to keep the cells viable.
    Description: This study was funded by the National Natural Science Foundation of China (41576138, 41076080, 41576138) to Dr. Jun-Rong Liang; the Woods Hole Center for Oceans and Human Health, National Science Foundation (OCE-1314642) to Dr. DonaldM Anderson; the National Institute of Environmental Health Sciences (1-P01-ES021923- 01) to Dr. DonaldM Anderson; and the ERC Advanced Award Diatomite and ANR project DiaDomOil to Dr. Chris Bowler.
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 45
    facet.materialart.
    Unknown
    Positive feedbacks enhance macroalgal resilience on degraded coral reefs (2017)
    Public Library of Science
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 11 (2016): e0155049, doi:10.1371/journal.pone.0155049.
    Description: Many reefs have shifted from coral and fish dominated habitats to less productive macroalgal dominated habitats, and current research is investigating means of reversing this phase shift. In the tropical Pacific, overfished reefs with inadequate herbivory can become dominated by the brown alga Sargassum polycystum. This alga suppresses recruitment and survival of corals and fishes, thus limiting the potential for reef recovery. Here we investigate the mechanisms that reinforce S. polycystum dominance and show that in addition to negatively affecting other species, this species acts in a self-reinforcing manner, positively promoting survival and growth of conspecifics. We found that survival and growth of both recruit-sized and mature S. polycystum fronds were higher within Sargassum beds than outside the beds and these results were found in both protected and fished reefs. Much of this benefit resulted from reduced herbivory within the Sargassum beds, but adult fronds also grew ~50% more within the beds even when herbivory did not appear to be occurring, suggesting some physiological advantage despite the intraspecific crowding. Thus via positive feedbacks, S. polycystum enhances its own growth and resistance to herbivores, facilitating its dominance (perhaps also expansion) and thus its resilience on degraded reefs. This may be a key feedback mechanism suppressing the recovery of coral communities in reefs dominated by macroalgal beds.
    Description: Financial support came to MEH from the National Science Foundation (OCE 0929119), the National Institutes of Health (2 U19 TW007401-10), and the Teasley Endowment to the Georgia Institute of Technology.
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 46
    facet.materialart.
    Unknown
    Preservation of three-dimensional spatial structure in the gut microbiome (2017)
    Public Library of Science
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 12 (2017): e0188257, doi:10.1371/journal.pone.0188257.
    Description: Preservation of three-dimensional structure in the gut is necessary in order to analyze the spatial organization of the gut microbiota and gut luminal contents. In this study, we evaluated preparation methods for mouse gut with the goal of preserving micron-scale spatial structure while performing fluorescence imaging assays. Our evaluation of embedding methods showed that commonly used media such as Tissue-Tek Optimal Cutting Temperature (OCT) compound, paraffin, and polyester waxes resulted in redistribution of luminal contents. By contrast, a hydrophilic methacrylate resin, Technovit H8100, preserved three-dimensional organization. Our mouse intestinal preparation protocol optimized using the Technovit H8100 embedding method was compatible with microbial fluorescence in situ hybridization (FISH) and other labeling techniques, including immunostaining and staining with both wheat germ agglutinin (WGA) and 4', 6-diamidino-2-phenylindole (DAPI). Mucus could be visualized whether the sample was fixed with paraformaldehyde (PFA) or with Carnoy’s fixative. The protocol optimized in this study enabled simultaneous visualization of micron-scale spatial patterns formed by microbial cells in the mouse intestines along with biogeographical landmarks such as host-derived mucus and food particles.
    Description: Funding provided by National Science Foundation (www.nsf.gov) grant 1650141 to J.L.M.W. and National Institutes of Health National Institute of Dental and Craniofacial Research (www.nidcr.nih.gov) grant DE022586 to G.G.B.
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 47
    facet.materialart.
    Unknown
    Indoles induce metamorphosis in a broad diversity of jellyfish, but not in a crown jelly (Coronatae) (2018)
    Public Library of Science
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 12 (2017): e0188601, doi:10.1371/journal.pone.0188601.
    Description: Many animals go through one or more metamorphoses during their lives, however, the molecular underpinnings of metamorphosis across diverse species are not well understood. Medusozoa (Cnidaria) is a clade of animals with complex life cycles, these life cycles can include a polyp stage that metamorphoses into a medusa (jellyfish). Medusae are produced through a variety of different developmental mechanisms—in some species polyps bud medusae (Hydrozoa), in others medusae are formed through polyp fission (Scyphozoa), while in others medusae are formed through direct transformation of the polyp (Cubozoa). To better understand the molecular mechanisms that may coordinate these different forms of metamorphosis, we tested two compounds first identified to induce metamorphosis in the moon jellyfish Aurelia aurita (indomethacin and 5-methoxy-2-methylindole) on a broad diversity of medusozoan polyps. We discovered that indole-containing compounds trigger metamorphosis across a broad diversity of species. All tested discomedusan polyps metamorphosed in the presence of both compounds, including species representatives of several major lineages within the clade (Pelagiidae, Cyaneidae, both clades of Rhizostomeae). In a cubozoan, low levels of 5-methoxy-2-methylindole reliably induced complete and healthy metamorphosis. In contrast, neither compound induced medusa metamorphosis in a coronate scyphozoan, or medusa production in either hydrozoan tested. Our results support the hypothesis that metamorphosis is mediated by a conserved induction pathway within discomedusan scyphozoans, and possibly cubozoans. However, failure of these compounds to induce metamorphosis in a coronate suggests this induction mechanism may have been lost in this clade, or is convergent between Scyphozoa and Cubozoa.
    Description: National Science Foundation Graduate Research Fellowship (DGE - 1058262; https://www.nsfgrfp.org/general_resources/about) to RRH. Evo-Devo-Eco Network (IOS # 0955517; http://edenrcn.com/) Research Exchange Funds, awarded to RRH. National Science Foundation Rhode Island Established Program to Stimulate Competitive Graduate Research Fellowship to RRH (DEB-1256695; http://web.uri.edu/rinsfepscor/grad-fellowships/). Brown University Ecology and Evolutionary Biology Dissertation Development Grant from the Bushnell Research and Education Fund awarded to RRH.
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 48
    facet.materialart.
    Unknown
    Linking deep convection and phytoplankton blooms in the northern Labrador Sea in a changing climate (2018)
    Public Library of Science
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 13 (2018): e0191509, doi:10.1371/journal.pone.0191509.
    Description: Wintertime convective mixing plays a pivotal role in the sub-polar North Atlantic spring phytoplankton blooms by favoring phytoplankton survival in the competition between light-dependent production and losses due to grazing and gravitational settling. We use satellite and ocean reanalyses to show that the area-averaged maximum winter mixed layer depth is positively correlated with April chlorophyll concentration in the northern Labrador Sea. A simple theoretical framework is developed to understand the relative roles of winter/spring convection and gravitational sedimentation in spring blooms in this region. Combining climate model simulations that project a weakening of wintertime Labrador Sea convection from Arctic sea ice melt with our framework suggests a potentially significant reduction in the initial fall phytoplankton population that survive the winter to seed the region’s spring bloom by the end of the 21st century.
    Description: KB, LB, PJR and LRL were supported by the Office of Science (BER), U. S. Department of Energy as part of the Regional and Global Climate Modelling (RGCM) Program. SCD acknowledges support from NASA Award NNX15AE65G North Atlantic Aerosol and Marine Ecosystem Study (NAAMES).
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 49
    facet.materialart.
    Unknown
    Prion protein inhibits fast axonal transport through a mechanism involving casein kinase 2 (2018)
    Public Library of Science
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 12 (2017): e0188340, doi:10.1371/journal.pone.0188340.
    Description: Prion diseases include a number of progressive neuropathies involving conformational changes in cellular prion protein (PrPc) that may be fatal sporadic, familial or infectious. Pathological evidence indicated that neurons affected in prion diseases follow a dying-back pattern of degeneration. However, specific cellular processes affected by PrPc that explain such a pattern have not yet been identified. Results from cell biological and pharmacological experiments in isolated squid axoplasm and primary cultured neurons reveal inhibition of fast axonal transport (FAT) as a novel toxic effect elicited by PrPc. Pharmacological, biochemical and cell biological experiments further indicate this toxic effect involves casein kinase 2 (CK2) activation, providing a molecular basis for the toxic effect of PrPc on FAT. CK2 was found to phosphorylate and inhibit light chain subunits of the major motor protein conventional kinesin. Collectively, these findings suggest CK2 as a novel therapeutic target to prevent the gradual loss of neuronal connectivity that characterizes prion diseases.
    Description: This work was supported by Alzheimer Association New Investigator Research Grant to Promote Diversity NIRGD-11-206379 and Consejo Nacional de Investigaciones Científicas y Técnicas PIP 112 20150100954 CO (to GP), National Institutes of Health NS066942A and NS096642 (to GM), R01-NS023868 and R01-NS041170 (to STB).
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 50
    facet.materialart.
    Unknown
    Cells containing aragonite crystals mediate responses to gravity in Trichoplax adhaerens (Placozoa), an animal lacking neurons and synapses (2018)
    Public Library of Science
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 13 (2018): e0190905, doi:10.1371/journal.pone.0190905.
    Description: Trichoplax adhaerens has only six cell types. The function as well as the structure of crystal cells, the least numerous cell type, presented an enigma. Crystal cells are arrayed around the perimeter of the animal and each contains a birefringent crystal. Crystal cells resemble lithocytes in other animals so we looked for evidence they are gravity sensors. Confocal microscopy showed that their cup-shaped nuclei are oriented toward the edge of the animal, and that the crystal shifts downward under the influence of gravity. Some animals spontaneously lack crystal cells and these animals behaved differently upon being tilted vertically than animals with a typical number of crystal cells. EM revealed crystal cell contacts with fiber cells and epithelial cells but these contacts lacked features of synapses. EM spectroscopic analyses showed that crystals consist of the aragonite form of calcium carbonate. We thus provide behavioral evidence that Trichoplax are able to sense gravity, and that crystal cells are likely to be their gravity receptors. Moreover, because placozoans are thought to have evolved during Ediacaran or Cryogenian eras associated with aragonite seas, and their crystals are made of aragonite, they may have acquired gravity sensors during this early era.
    Description: This research was supported by the intramural research program of the NIH, NINDS.
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 51
    facet.materialart.
    Unknown
    The use of mesoscale eddies by juvenile loggerhead sea turtles (Caretta caretta) in the southwestern Atlantic (2017)
    Public Library of Science
    Details
    Publication Date: 2022-05-26
    Description: This is an open access article, free of all copyright. The definitive version was published in PLoS ONE 12 (2017): e0172839, doi:10.1371/journal.pone.0172839.
    Description: Marine animals, such as turtles, seabirds and pelagic fishes, are observed to travel and congregate around eddies in the open ocean. Mesoscale eddies, large swirling ocean vortices with radius scales of approximately 50–100 km, provide environmental variability that can structure these populations. In this study, we investigate the use of mesoscale eddies by 24 individual juvenile loggerhead sea turtles (Caretta caretta) in the Brazil-Malvinas Confluence region. The influence of eddies on turtles is assessed by collocating the turtle trajectories to the tracks of mesoscale eddies identified in maps of sea level anomaly. Juvenile loggerhead sea turtles are significantly more likely to be located in the interiors of anticyclones in this region. The distribution of surface drifters in eddy interiors reveals no significant association with the interiors of cyclones or anticyclones, suggesting higher prevalence of turtles in anticyclones is a result of their behavior. In the southern portion of the Brazil-Malvinas Confluence region, turtle swimming speed is significantly slower in the interiors of anticyclones, when compared to the periphery, suggesting that these turtles are possibly feeding on prey items associated with anomalously low near-surface chlorophyll concentrations observed in those features.
    Description: A Woods Hole Postdoctoral Fellowship awarded to PG and NASA grant NNX13AE47G funded this work. CB is grateful for support from NOAA and the NSF-GRFP (Grant No. 1314109). DJM gratefully acknowledges support from NASA and NSF.
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 52
    facet.materialart.
    Unknown
    Hurricane Isaac brings more than oil ashore: Characteristics of beach deposits following the Deepwater Horizon spill. (2019)
    Public Library of Science
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Lemkau, K. L., Reddy, C. M., Carmichael, C. A., Aeppli, C., Swarthout, R. F., & White, H. K. Hurricane Isaac brings more than oil ashore: Characteristics of beach deposits following the Deepwater Horizon spill. Plos One, 14(3), (2019):e0213464, doi:10.1371/journal.pone.0213464.
    Description: Prior to Hurricane Isaac making landfall along the Gulf of Mexico coast in August 2012, local and state officials were concerned that the hurricane would mobilize submerged oiled-materials from the Deepwater Horizon (DWH) spill. In this study, we investigated materials washed ashore following the hurricane to determine if it affected the chemical composition or density of oil-containing sand patties regularly found on Gulf Coast beaches. While small changes in sand patty density were observed in samples collected before and after the hurricane, these variations appear to have been driven by differences in sampling location and not linked to the passing of Hurricane Isaac. Visual and chemical analysis of sand patties confirmed that the contents was consistent with oil from the Macondo well. Petroleum hydrocarbon signatures of samples collected before and after the hurricane showed no notable changes. In the days following Hurricane Isaac, dark-colored mats were also found on the beach in Fort Morgan, AL, and community reports speculated that these mats contained oil from the DWH spill. Chemical analysis of these mat samples identified n-alkanes but no other petroleum hydrocarbons. Bulk and δ13C organic carbon analyses indicated mat samples were comprised of marshland peat and not related to the DWH spill. This research indicates that Hurricane Isaac did not result in a notable change the composition of oil delivered to beaches at the investigated field sites. This study underscores the need for improved communications with interested stakeholders regarding how to differentiate oiled from non-oiled materials. This is especially important given the high cost of removing oiled debris and the increasing likelihood of false positives as oiled-materials washing ashore from a spill become less abundant over time.
    Description: The authors wish to acknowledge support for this project from the Gulf of Mexico Research Initiative (RFP-V), the Deep-C Consortium (SA 16-30), NSF (OCE-1333148) awarded to CMR, and a Gulf Research Program Early-Career Research Fellowship to HKW. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 53
    facet.materialart.
    Unknown
    From the track to the ocean : using flow control to improve marine bio-logging tags for cetaceans (2017)
    Public Library of Science
    Details
    Publication Date: 2022-05-26
    Description: This is an open access article, free of all copyright. The definitive version was published in PLoS ONE 12 (2017): e0170962, doi:10.1371/journal.pone.0170962.
    Description: Bio-logging tags are an important tool for the study of cetaceans, but superficial tags inevitably increase hydrodynamic loading. Substantial forces can be generated by tags on fast-swimming animals, potentially affecting behavior and energetics or promoting early tag removal. Streamlined forms have been used to reduce loading, but these designs can accelerate flow over the top of the tag. This non-axisymmetric flow results in large lift forces (normal to the animal) that become the dominant force component at high speeds. In order to reduce lift and minimize total hydrodynamic loading this work presents a new tag design (Model A) that incorporates a hydrodynamic body, a channel to reduce fluid speed differences above and below the housing and wing to redirect flow to counter lift. Additionally, three derivatives of the Model A design were used to examine the contribution of individual flow control features to overall performance. Hydrodynamic loadings of four models were compared using computational fluid dynamics (CFD). The Model A design eliminated all lift force and generated up to ~30 N of downward force in simulated 6 m/s aligned flow. The simulations were validated using particle image velocimetry (PIV) to experimentally characterize the flow around the tag design. The results of these experiments confirm the trends predicted by the simulations and demonstrate the potential benefit of flow control elements for the reduction of tag induced forces on the animal.
    Description: This project was funded by the National Oceanographic Partnership Program [National Science Foundation via the Office of Naval Research N00014-11-1-0113]. C. Spencer Garborg was supported by a Grove City College Swezey Student Fellowship to Erik Anderson. Mark Johnson was funded by a Marie Curie-Sklodowska grant from the European Union.
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 54
    facet.materialart.
    Unknown
    Fukushima Daiichi–derived radionuclides in the ocean : transport, fate, and impacts (2017)
    Annual Reviews
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Annual Review of Marine Science 9 (2017): 173-203, doi:10.1146/annurev-marine-010816-060733.
    Description: The events that followed the Tohoku earthquake and tsunami on March 11, 2011, included the loss of power and overheating at the Fukushima Daiichi nuclear power plants, which led to extensive releases of radioactive gases, volatiles, and liquids, particularly to the coastal ocean. The fate of these radionuclides depends in large part on their oceanic geochemistry, physical processes, and biological uptake. Whereas radioactivity on land can be resampled and its distribution mapped, releases to the marine environment are harder to characterize owing to variability in ocean currents and the general challenges of sampling at sea. Five years later, it is appropriate to review what happened in terms of the sources, transport, and fate of these radionuclides in the ocean. In addition to the oceanic behavior of these contaminants, this review considers the potential health effects and societal impacts.
    Description: K.B. was supported in part by the Gordon and Betty Moore Foundation and the Deerbrook Charitable Trust. P.M. was supported in part by the Generalitat de Catalunya through MERS (grant 2014 SGR 1356), the European Commission 7th Framework COMET-FRAME project (grant agreement 604974), and the Ministerio de Economía y Competitividad of Spain (project CTM2011-15152-E). S.C. was supported in part by the French program Investissement d'Avenir run by the National Research Agency (AMORAD project, grant ANR-11-RSNR-0002). D.O. was supported in part by the Center for Environmental Radioactivity (NFR Centers of Excellence grant 223268/F50). J.N.S. was supported in part by the Marine Environmental Observation, Prediction, and Response Network.
    Keywords: Cesium ; Caesium ; North Pacific ; Radioactivity ; Japan
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 55
    facet.materialart.
    Unknown
    Evidence of molting and the function of “rock-nosing” behavior in bowhead whales in the eastern Canadian Arctic (2017)
    Public Library of Science
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 12 (2017): e0186156, doi:10.1371/journal.pone.0186156.
    Description: Bowhead whales (Balaena mysticetus) have a nearly circumpolar distribution, and occasionally occupy warmer shallow coastal areas during summertime that may facilitate molting. However, relatively little is known about the occurrence of molting and associated behaviors in bowhead whales. We opportunistically observed whales in Cumberland Sound, Nunavut, Canada with skin irregularities consistent with molting during August 2014, and collected a skin sample from a biopsied whale that revealed loose epidermis and sloughing. During August 2016, we flew a small unmanned aerial system (sUAS) over whales to take video and still images to: 1) determine unique individuals; 2) estimate the proportion of the body of unique individuals that exhibited sloughing skin; 3) determine the presence or absence of superficial lines representative of rock-rubbing behavior; and 4) measure body lengths to infer age-class. The still images revealed that all individuals (n = 81 whales) were sloughing skin, and that nearly 40% of them had mottled skin over more than two-thirds of their bodies. The video images captured bowhead whales rubbing on large rocks in shallow, coastal areas—likely to facilitate molting. Molting and rock rubbing appears to be pervasive during late summer for whales in the eastern Canadian Arctic.
    Description: Fieldwork was funded by: Fisheries and Oceans Canada (Emerging Fisheries 41436-810-120-4D875), Nunavut Wildlife Research Trust Fund (project 3-13-29 Bowhead Whale Movement's and Ecology), Molson Foundation (318366), Ocean Tracking Network (NSERC NETGP 375118-08), and ArcticNet Centre of Excellence (317588) awarded to S.H. Ferguson and World Wildlife Fund Canada (Arctic Species Conservation Fund) awarded to W.R. Koski and S.M.E. Fortune. Additional field work support was provided by: U.S. Department of the Interior, Minerals Management Service (MMS; now Bureau of Ocean Energy Management), through Inter-agency Agreement No. M08PG20021 with the U.S. Department of Commerce, National Oceanic and Atmospheric Administration, as part of the MMS Alaska Environmental Studies Program awarded to M.F. Baumgartner. Personnel support was provided by: Natural Sciences and Engineering Research Council Canadian Graduate Scholarship, the W. Garfield Weston Award for Northern Research, University of British Columbia Affiliated Fellowship and Northern Scientific Training Program (Canadian Polar Commission) awarded to S.M.E. Fortune
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 56
    facet.materialart.
    Unknown
    Short-term effect of simulated salt marsh restoration by sand-amendment on sediment bacterial communities (2019)
    Public Library of Science
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Thomas, F., Morris, J. T., Wigand, C., & Sievert, S. M. Short-term effect of simulated salt marsh restoration by sand-amendment on sediment bacterial communities. Plos One, 14(4), (2019):e0215767, doi:10.1371/journal.pone.0215767.
    Description: Coastal climate adaptation strategies are needed to build salt marsh resiliency and maintain critical ecosystem services in response to impacts caused by climate change. Although resident microbial communities perform crucial biogeochemical cycles for salt marsh functioning, their response to restoration practices is still understudied. One promising restoration strategy is the placement of sand or sediment onto the marsh platform to increase marsh resiliency. A previous study examined the above- and below-ground structure, soil carbon dioxide emissions, and pore water constituents in Spartina alterniflora-vegetated natural marsh sediments and sand-amended sediments at varying inundation regimes. Here, we analyzed samples from the same experiment to test the effect of sand-amendments on the microbial communities after 5 months. Along with the previously observed changes in biogeochemistry, sand amendments drastically modified the bacterial communities, decreasing richness and diversity. The dominant sulfur-cycling bacterial community found in natural sediments was replaced by one dominated by iron oxidizers and aerobic heterotrophs, the abundance of which correlated with higher CO2-flux. In particular, the relative abundance of iron-oxidizing Zetaproteobacteria increased in the sand-amended sediments, possibly contributing to acidification by the formation of iron oxyhydroxides. Our data suggest that the bacterial community structure can equilibrate if the inundation regime is maintained within the optimal range for S. alterniflora. While long-term effects of changes in bacterial community on the growth of S. alterniflora are not clear, our results suggest that analyzing the microbial community composition could be a useful tool to monitor climate adaptation and restoration efforts.
    Description: This work was supported by NSF grants DEB-1050557 (SMS) and OCE-1637630 (JM), and WHOI Investment in Science Funds (SMS). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 57
    facet.materialart.
    Unknown
    Evaluating coral trophic strategies using fatty acid composition and indices (2019)
    Public Library of Science
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Radice, V. Z., Brett, M. T., Fry, B., Fox, M. D., Hoegh-Guldberg, O., & Dove, S. G. Evaluating coral trophic strategies using fatty acid composition and indices. Plos One, 14(9), (2019): e0222327, doi:10.1371/journal.pone.0222327.
    Description: The ecological success of shallow water reef-building corals has been linked to the symbiosis between the coral host and its dinoflagellate symbionts (herein ‘symbionts’). As mixotrophs, symbiotic corals depend on nutrients 1) transferred from their photosynthetic symbionts (autotrophy) and 2) acquired by host feeding on particulate organic resources (heterotrophy). However, coral species differ in the extent to which they depend on heterotrophy for nutrition and these differences are typically poorly defined. Here, a multi-tracer fatty acid approach was used to evaluate the trophic strategies of three species of common reef-building coral (Galaxea fascicularis, Pachyseris speciosa, and Pocillopora verrucosa) whose trophic strategies had previously been identified using carbon stable isotopes. The composition and various indices of fatty acids were compared to examine the relative contribution of symbiont autotrophy and host heterotrophy in coral energy acquisition. A linear discriminant analysis (LDA) was used to estimate the contribution of polyunsaturated fatty acids (PUFA) derived from various potential sources to the coral hosts. The total fatty acid composition and fatty acid indices revealed differences between the more heterotrophic (P. verrucosa) and more autotrophic (P. speciosa) coral hosts, with the coral host G. fascicularis showing overlap with the other two species and greater variability overall. For the more heterotrophic P. verrucosa, the fatty acid indices and LDA results both indicated a greater proportion of copepod-derived fatty acids compared to the other coral species. Overall, the LDA estimated that PUFA derived from particulate resources (e.g., copepods and diatoms) comprised a greater proportion of coral host PUFA in contrast to the lower proportion of symbiont-derived PUFA. These estimates provide insight into the importance of heterotrophy in coral nutrition, especially in productive reef systems. The study supports carbon stable isotope results and demonstrates the utility of fatty acid analyses for exploring the trophic strategies of reef-building corals.
    Description: This study was made possible by funding from the XL Catlin Seaview Survey (OHG and VZR; http://catlinseaviewsurvey.com/), Australian Research Council (ARC) Centre of Excellence for Coral Reef Studies (CE140100020; SD and OHG; https://www.coralcoe.org.au/), an ARC Laureate Fellowship (FL120100066; OHG; https://www.arc.gov.au), the University of Queensland Research Training Scholarship (VZR; https://www.uq.edu.au/), and the University of Washington Dale A. Carlson Endowed Faculty Support Fund (MTB and VZR; https://www.washington.edu/). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 58
    facet.materialart.
    Unknown
    Ventilation of the Deep Ocean Carbon Reservoir During the Last Deglaciation: Results From the Southeast Pacific (2019)
    American Geophysical Union (AGU)
    In:  EPIC3Paleoceanography and Paleoclimatology, American Geophysical Union (AGU), 34(12), pp. 2080-2097, ISSN: 2572-4517
    Details
    Publication Date: 2023-03-31
    Description: Coeval changes in atmospheric CO2 and 14C contents during the last deglaciation are often attributed to ocean circulation changes that released carbon stored in the deep ocean during the Last Glacial Maximum (LGM). Work is being done to generate records that allow for the identification of the exact mechanisms leading to the accumulation and release of carbon from the oceanic reservoir, but these mechanisms are still the subject of debate. Here we present foraminifera 14C data from five cores in a transect across the Chilean continental margin between ~540 and ~3,100 m depth spanning the last 20,000 years. Our data reveal that during the LGM, waters at ~2,000 m were 50% to 80% more depleted in Δ14C than waters at ~1,500 m when compared to modern values, consistent with the hypothesis of a glacial deep ocean carbon reservoir that was isolated from the atmosphere. During the deglaciation, our intermediate water records reveal homogenization in the Δ14C values between ~800 and ~1,500 m from ~16.5–14.5 ka cal BP to ~14–12 ka cal BP, which we interpret as deeper penetration of Antarctic Intermediate Water. While many questions still remain, this process could aid the ventilation of the deep ocean at the beginning of the deglaciation, contributing to the observed ~40 ppm rise in atmospheric pCO2.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , peerRev
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 59
    facet.materialart.
    Unknown
    Retrieval of Wintertime Sea Ice Production in Arctic Polynyas Using Thermal Infrared and Passive Microwave Remote Sensing Data (2019)
    American Geophysical Union (AGU)
    In:  EPIC3Journal of Geophysical Research: Oceans, American Geophysical Union (AGU), 124(8), pp. 5503-5528, ISSN: 2169-9275
    Details
    Publication Date: 2022-11-02
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , NonPeerReviewed
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 60
    facet.materialart.
    Unknown
    Concentrations and Water Mass Transport of Legacy POPs in the Arctic Ocean (2018)
    American Geophysical Union (AGU)
    In:  EPIC3Geophysical Research Letters, American Geophysical Union (AGU), 45(23), pp. 12972-12981, ISSN: 0094-8276
    Details
    Publication Date: 2023-01-30
    Description: The Arctic Ocean is known to be contaminated by various persistent organic pollutants (POPs). The Fram Strait, the only deepwater passage to the Arctic Ocean (from the Atlantic Ocean), represents an unquantified gateway for POPs fluxes into and out of the Arctic. Polyethylene passive samplers were deployed in vertical profiles in the Fram Strait and in air and surface water in the Canadian Archipelago to determine the concentrations, profiles, and mass fluxes of dissolved polychlorinated biphenyls (PCBs) and organochlorine pesticides. In the Fram Strait, higher concentrations of ΣPCBs (1.3–3.6 pg/L) and dichlorodiphenyltrichloroethanes (ΣDDTs, 5.2–9.1 pg/L) were observed in the deepwater masses (below 1,000 m), similar to nutrient-like vertical profiles. There was net southward transport of hexachlorobenzene and hexachlorocyclohexanes (ΣHCHs) of 0.70 and 14 Mg/year but a net northward transport of ΣPCBs at 0.16 Mg/year through the Fram Strait.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 61
    Electronic Resource
    Electronic Resource
    STRUCTURE AND FUNCTION OF LIPID-DNA COMPLEXES FOR GENE DELIVERY (2000)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 29 (2000), S. 27-47 
    Details
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Owing to the rapid development of in vivo applications for non-viral gene delivery vectors, it is necessary to have a better understanding of how the structure-activity relationships of these lipid-DNA complexes are affected by their environment. Indeed, research in gene therapy first focused on in vitro cell culture studies to determine the mechanisms involved in the delivery of DNA into the cell. New biophysical techniques such as electron microscopy and X-ray diffraction have been developed to discern the structure of the lipid-DNA complex. However, further studies have revealed discrepancies between optimal lipid-DNA formulations for in vitro transfection and for in vivo administration of these vectors. Furthermore, some immune stimulatory effects have been associated with in vivo lipid-DNA administration. This review summarizes the current state of knowledge on in vitro and in vivo lipid-DNA complex transfections. New prospects of vectors for in vivo gene transfer are also discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.biophys.29.1.27
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 62
    Electronic Resource
    Electronic Resource
    GCN5-RELATED N-ACETYLTRANSFERASES: A Structural Overview (2000)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 29 (2000), S. 81-103 
    Details
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Hundreds of acetyltransferases exist. All use a common acetyl donor-acetyl coenzyme A-and each exhibits remarkable specificity for acetyl acceptors, which include small molecules and proteins. Analysis of the primary sequences of these enzymes indicates that they can be sorted into several superfamilies. This review covers the three-dimensional structures of members of one of these superfamilies, now referred to in the literature as the GCN5-related N-acetyltransferases (GNAT), reflecting the importance of one functional category, the histone acetyltransferases. Despite the diversity of substrate specificities, members of the GNAT superfamily demonstrate remarkable similarity in protein topology and mode of acetyl coenzyme A binding, likely reflecting a conserved catalytic mechanism.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.biophys.29.1.81
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 63
    Electronic Resource
    Electronic Resource
    SIGNALING AND SUBCELLULAR TARGETING BY MEMBRANE-BINDING DOMAINS1 (2000)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 29 (2000), S. 49-79 
    Details
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Protein kinase C homology-1 and -2, FYVE, and pleckstrin homology domains are ubiquitous in eukaryotic signal transduction and membrane-trafficking proteins. These domains regulate subcellular localization and protein function by binding to lipid ligands embedded in cell membranes. Structural and biochemical analysis of these domains has shown that their molecular mechanisms of membrane binding depend on a combination of specific and nonspecific interactions with membrane lipids. In vivo studies of green fluorescent protein fusions have highlighted the key roles of these domains in regulating protein localization to plasma and internal membranes in cells.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.biophys.29.1.49
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 64
    Electronic Resource
    Electronic Resource
    MEASURING THE FORCES THAT CONTROL PROTEIN INTERACTIONS (2000)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 29 (2000), S. 1-26 
    Details
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Although the force fields and interaction energies that control protein behavior can be inferred indirectly from equilibrium and kinetic measurements, recent developments have made it possible to quantify directly (a) the ranges, magnitudes, and time dependence of the interaction energies and forces between biological materials; (b) the mechanical properties of isolated proteins; and (c) the strength of single receptor-ligand bonds. This review describes recent results obtained by using the atomic force microscope, optical tweezers, the surface force apparatus, and micropipette aspiration to quantify short-range protein-ligand interactions and the long-range, nonspecific forces that together control protein behavior. The examples presented illustrate the power of force measurements to quantify directly the force fields and energies that control protein behavior.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.biophys.29.1.1
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 65
    Electronic Resource
    Electronic Resource
    DNA RECOGNITION BY Cys2His2 ZINC FINGER PROTEINS (2000)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 29 (2000), S. 183-212 
    Details
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Cys2His2 zinc fingers are one of the most common DNA-binding motifs found in eukaryotic transcription factors. These proteins typically contain several fingers that make tandem contacts along the DNA. Each finger has a conserved betabetaalpha structure, and amino acids on the surface of the alpha-helix contact bases in the major groove. This simple, modular structure of zinc finger proteins, and the wide variety of DNA sequences they can recognize, make them an attractive framework for attempts to design novel DNA-binding proteins. Several studies have selected fingers with new specificities, and there clearly are recurring patterns in the observed side chain-base interactions. However, the structural details of recognition are intricate enough that there are no general rules (a "recognition code") that would allow the design of an optimal protein for any desired target site. Construction of multifinger proteins is also complicated by interactions between neighboring fingers and the effect of the intervening linker. This review analyzes DNA recognition by Cys2His2 zinc fingers and summarizes progress in generating proteins with novel specificities from fingers selected by phage display.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.biophys.29.1.183
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 66
    Electronic Resource
    Electronic Resource
    FAST KINETICS AND MECHANISMS IN PROTEIN FOLDING1 (2000)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 29 (2000), S. 327-359 
    Details
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract This review describes how kinetic experiments using techniques with dramatically improved time resolution have contributed to understanding mechanisms in protein folding. Optical triggering with nanosecond laser pulses has made it possible to study the fastest-folding proteins as well as fundamental processes in folding for the first time. These include formation of alpha-helices, beta-sheets, and contacts between residues distant in sequence, as well as overall collapse of the polypeptide chain. Improvements in the time resolution of mixing experiments and the use of dynamic nuclear magnetic resonance methods have also allowed kinetic studies of proteins that fold too fast (〉 103 s-1) to be observed by conventional methods. Simple statistical mechanical models have been extremely useful in interpreting the experimental results. One of the surprises is that models originally developed for explaining the fast kinetics of secondary structure formation in isolated peptides are also successful in calculating folding rates of single domain proteins from their native three-dimensional structure.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.biophys.29.1.327
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 67
    Electronic Resource
    Electronic Resource
    A DECADE OF CLC CHLORIDE CHANNELS: Structure, Mechanism, and Many Unsettled Questions (2000)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 29 (2000), S. 411-438 
    Details
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract ClC-type chloride channels are ubiquitous throughout the biological world. Expressed in nearly every cell type, these proteins have a host of biological functions. With nine distinct homologues known in eukaryotes, the ClCs represent the only molecularly defined family of chloride channels. ClC channels exhibit features of molecular architecture and gating mechanisms unprecedented in other types of ion channels. They form two-pore homodimers, and their voltage-dependence arises not from charged residues in the protein, but rather via coupling of gating to the movement of chloride ions within the pore. Because the functional characteristics of only a few ClC channels have been studied in detail, we are still learning which properties are general to the whole family. New approaches, including structural analyses, will be crucial to an understanding of ClC architecture and function.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.biophys.29.1.411
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 68
    Electronic Resource
    Electronic Resource
    DESIGNED SEQUENCE-SPECIFIC MINOR GROOVE LIGANDS (2000)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 29 (2000), S. 439-461 
    Details
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract In the past decade, a general design for sequence-specific minor groove ligands has evolved, based on the natural products distamycin and netropsin. By utilizing a basic set of design rules for connecting pyrrole, imidazole, and hydroxypyrrole modules, new ligands can be prepared to target almost any sequence of interest with both high affinity and specificity. In this review we present the design rules with a brief history of how they evolved. The structural basis for sequence-specific recognition is explained, together with developments that allow linking of recognition modules that enable targeting of long DNA sequences. Examples of the affinity and specificity that can be achieved with a number of variations on the basic design are given. Recently these molecules have been used to compete with proteins both in vitro and in vivo, and a brief description of the experimental results are given.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.biophys.29.1.439
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 69
    Electronic Resource
    Electronic Resource
    NMR PROBES OF MOLECULAR DYNAMICS: Overview and Comparison with Other Techniques (2001)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 30 (2001), S. 129-155 
    Details
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract NMR spin relaxation spectroscopy is a powerful approach for characterizing intramolecular and overall rotational motions in proteins. This review describes experimental methods for measuring laboratory frame spin relaxation rate constants by high-resolution solution-state NMR spectroscopy, together with theoretical approaches for interpreting spin relaxation data in order to quantify protein conformational dynamics on picosecond-nanosecond time scales. Recent applications of these techniques to proteins are surveyed, and investigations of the contribution of conformational chain entropy to protein function are highlighted. Insights into the dynamical properties of proteins obtained from NMR spin relaxation spectroscopy are compared with results derived from other experimental and theoretical techniques.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.biophys.30.1.129
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 70
    Electronic Resource
    Electronic Resource
    STRUCTURE OF PROTEINS INVOLVED IN SYNAPTIC VESICLE FUSION IN NEURONS (2001)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 30 (2001), S. 157-171 
    Details
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract The fusion of vesicles with target membranes is controlled by a complex network of protein-protein and protein-lipid interactions. Structures of the SNARE complex, synaptotagmin III, nSec1, domains of the NSF chaperone and its adaptor SNAP, and Rab3 and some of its effectors provide the framework for developing molecular models of vesicle fusion and for designing experiments to test these models.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.biophys.30.1.157
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 71
    Electronic Resource
    Electronic Resource
    AB INITIO PROTEIN STRUCTURE PREDICTION: Progress and Prospects (2001)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 30 (2001), S. 173-189 
    Details
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Considerable recent progress has been made in the field of ab initio protein structure prediction, as witnessed by the third Critical Assessment of Structure Prediction (CASP3). In spite of this progress, much work remains, for the field has yet to produce consistently reliable ab initio structure prediction protocols. In this work, we review the features of current ab initio protocols in an attempt to highlight the foundations of recent progress in the field and suggest promising directions for future work.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.biophys.30.1.173
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 72
    Electronic Resource
    Electronic Resource
    STRUCTURAL RELATIONSHIPS AMONG REGULATED AND UNREGULATED PHOSPHORYLASES (2001)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 30 (2001), S. 191-209 
    Details
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Species and tissue-specific isozymes of phosphorylase display differences in regulatory properties consistent with their distinct roles in particular organisms and tissues. In this review, we compare crystallographic structures of regulated and unregulated phosphorylases, including maltodextrin phosphorylase (MalP) from Escherichia coli, glycogen phosphorylase from yeast, and mammalian isozymes from muscle and liver tissues. Mutagenesis and functional studies supplement the structural work and provide insights into the structural basis for allosteric control mechanisms. MalP, a simple, unregulated enzyme, is contrasted with the more complicated yeast and mammalian phosphorylases that have evolved regulatory sites onto the basic catalytic architecture. The human liver and muscle isozymes show differences structurally in their means of invoking allosteric activation. Phosphorylation, though common to both the yeast and mammalian enzymes, occurs at different sites and activates the enzymes by surprisingly different mechanisms.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.biophys.30.1.191
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 73
    Electronic Resource
    Electronic Resource
    BIOMOLECULAR SIMULATIONS: Recent Developments in Force Fields, Simulations of Enzyme Catalysis, Protein-Ligand, Protein-Protein, and Protein-Nucleic Acid Noncovalent Interactions (2001)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 30 (2001), S. 211-243 
    Details
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Computer modeling has been developed and widely applied in studying molecules of biological interest. The force field is the cornerstone of computer simulations, and many force fields have been developed and successfully applied in these simulations. Two interesting areas are (a) studying enzyme catalytic mechanisms using a combination of quantum mechanics and molecular mechanics, and (b) studying macromolecular dynamics and interactions using molecular dynamics (MD) and free energy (FE) calculation methods. Enzyme catalysis involves forming and breaking of covalent bonds and requires the use of quantum mechanics. Noncovalent interactions appear ubiquitously in biology, but here we confine ourselves to review only noncovalent interactions between protein and protein, protein and ligand, and protein and nucleic acids.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.biophys.30.1.211
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 74
    Electronic Resource
    Electronic Resource
    CHAPERONIN-MEDIATED PROTEIN FOLDING (2001)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 30 (2001), S. 245-269 
    Details
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Molecular chaperones are required to assist folding of a subset of proteins in Escherichia coli. We describe a conceptual framework for understanding how the GroEL-GroES system assists misfolded proteins to reach their native states. The architecture of GroEL consists of double toroids stacked back-to-back. However, most of the fundamentals of the GroEL action can be described in terms of the single ring. A key idea in our framework is that, with coordinated ATP hydrolysis and GroES binding, GroEL participates actively by repeatedly unfolding the substrate protein (SP), provided that it is trapped in one of the misfolded states. We conjecture that the unfolding of SP becomes possible because a stretching force is transmitted to the SP when the GroEL particle undergoes allosteric transitions. Force-induced unfolding of the SP puts it on a higher free-energy point in the multidimensional energy landscape from which the SP can either reach the native conformation with some probability or be trapped in one of the competing basins of attraction (i.e., the SP undergoes kinetic partitioning). The model shows, in a natural way, that the time scales in the dynamics of the allosteric transitions are intimately coupled to folding rates of the SP. Several scenarios for chaperonin-assisted folding emerge depending on the interplay of the time scales governing the cycle. Further refinement of this framework may be necessary because single molecule experiments indicate that there is a great dispersion in the time scales governing the dynamics of the chaperonin cycle.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.biophys.30.1.245
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 75
    Electronic Resource
    Electronic Resource
    MY ROAD TO BIOPHYSICS: Picking Flowers on the Way to Photosynthesis (2002)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 31 (2002), S. 1-44 
    Details
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.biophys.31.082901.134147
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 76
    Electronic Resource
    Electronic Resource
    PROPERTIES AND BIOLOGICAL ACTIVITIES OF THIOREDOXINS (2001)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 30 (2001), S. 421-455 
    Details
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract The mammalian thioredoxins are a family of small (approximately 12 kDa) redox proteins that undergo NADPH-dependent reduction by thioredoxin reductase and in turn reduce oxidized cysteine groups on proteins. The two main thioredoxins are thioredoxin-1, a cytosolic and nuclear form, and thioredoxin-2, a mitochondrial form. Thioredoxin-1 has been studied more. It performs many biological actions including the supply of reducing equivalents to thioredoxin peroxidases and ribonucleotide reductase, the regulation of transcription factor activity, and the regulation of enzyme activity by heterodimer formation. Thioredoxin-1 stimulates cell growth and is an inhibitor of apoptosis. Thioredoxins may play a role in a variety of human diseases including cancer. An increased level of thioredoxin-1 is found in many human tumors, where it is associated with aggressive tumor growth. Drugs are being developed that inhibit thioredoxin and that have antitumor activity.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.biophys.30.1.421
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 77
    Electronic Resource
    Electronic Resource
    NMR STUDIES OF LIPOPROTEIN STRUCTURE (2002)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 31 (2002), S. 177-206 
    Details
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Early NMR structural studies of serum lipoproteins were based on 1H, 13C, 31P, and 2H studies of lipid components. From the early studies information on composition, lipid chain dynamics and order parameters, and monolayer organization resulted. More recently, selective or complete isotopic labeling techniques, combined with multidimensional NMR spectroscopy, have resulted in structural information of apoprotein fragments. Finally, use of heteronuclear three- and four-dimensional experiments have yielded solution structures and protein-lipid interactions of intact apolipoproteins C-I, C-II, and A-I.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.biophys.31.101101.140910
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 78
    Electronic Resource
    Electronic Resource
    THE LINKAGE BETWEEN PROTEIN FOLDING AND FUNCTIONAL COOPERATIVITY: Two Sides of the Same Coin? (2002)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 31 (2002), S. 235-256 
    Details
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract During the course of their biological function, proteins undergo different types of structural rearrangements ranging from local to large-scale conformational changes. These changes are usually triggered by their interactions with small-molecular-weight ligands or other macromolecules. Because binding interactions occur at specific sites and involve only a small number of residues, a chain of cooperative interactions is necessary for the propagation of binding signals to distal locations within the protein structure. This process requires an uneven structural distribution of protein stability and cooperativity as revealed by NMR-detected hydrogen/deuterium exchange experiments under native conditions. The distribution of stabilizing interactions does not only provide the architectural foundation to the three-dimensional structure of a protein, but it also provides the required framework for functional cooperativity. In this review, the statistical thermodynamic linkage between protein stability, functional cooperativity, and ligand binding is discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.biophys.31.082901.134215
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 79
    Electronic Resource
    Electronic Resource
    INTERPRETING THE EFFECTS OF SMALL UNCHARGED SOLUTES ON PROTEIN-FOLDING EQUILIBRIA (2001)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 30 (2001), S. 271-306 
    Details
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Proteins are designed to function in environments crowded by cosolutes, but most studies of protein equilibria are conducted in dilute solution. While there is no doubt that crowding changes protein equilibria, interpretations of the changes remain controversial. This review combines experimental observations on the effect of small uncharged cosolutes (mostly sugars) on protein stability with a discussion of the thermodynamics of cosolute-induced nonideality and critical assessments of the most commonly applied interpretations. Despite the controversy surrounding the most appropriate manner for interpreting these effects of thermodynamic nonideality arising from the presence of small cosolutes, experimental advantage may still be taken of the ability of the cosolute effect to promote not only protein stabilization but also protein self-association and complex formation between dissimilar reactants. This phenomenon clearly has potential ramifications in the cell, where the crowded environment could well induce the same effects.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.biophys.30.1.271
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 80
    Electronic Resource
    Electronic Resource
    BINDING OF LIGANDS AND ACTIVATION OF TRANSCRIPTION BY NUCLEAR RECEPTORS (2001)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 30 (2001), S. 329-359 
    Details
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Nuclear receptors (NRs) form a superfamily of ligand-inducible transcription factors composed of several domains. Recent structural studies focused on domain E, which harbors the ligand-binding site and the ligand-dependent transcription activation function AF-2. Structures of single representatives in an increasing number of various complexes as well as new structures of further NRs addressed issues such as discrimination of ligands, superagonism, isotype specificity, and partial agonism. Until today, one unique transcriptionally active form of domain E was determined; however, divergent tertiary structures of apo-forms and transcriptionally inactive forms are known. Thus, recent results link the transformation of NRs upon ligand binding to principles of protein folding. Furthermore, the ensemble of NR structures, including those of DNA-binding domains, provides one of the foundations for the understanding of interactions with transcription intermediary factors up to the characterization of the link between NR complexes and the basal transcriptional machinery at the structural level.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.biophys.30.1.329
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 81
    Electronic Resource
    Electronic Resource
    STRUCTURAL INSIGHTS INTO MICROTUBULE FUNCTION (2001)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 30 (2001), S. 397-420 
    Details
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Microtubules are polymers that are essential for, among other functions, cell transport and cell division in all eukaryotes. The regulation of the microtubule system includes transcription of different tubulin isotypes, folding of alpha/beta-tubulin heterodimers, post-translation modification of tubulin, and nucleotide-based microtubule dynamics, as well as interaction with numerous microtubule-associated proteins that are themselves regulated. The result is the precise temporal and spatial pattern of microtubules that is observed throughout the cell cycle. The recent high-resolution analysis of the structure of tubulin and the microtubule has brought new insight to the study of microtubule function and regulation, as well as the mode of action of antimitotic drugs that disrupt normal microtubule behavior. The combination of structural, genetic, biochemical, and biophysical data should soon give us a fuller understanding of the exquisite details in the regulation of the microtubule cytoskeleton.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.biophys.30.1.397
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 82
    Electronic Resource
    Electronic Resource
    RIBOZYME STRUCTURES AND MECHANISMS (2001)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 30 (2001), S. 457-475 
    Details
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract The past few years have seen exciting advances in understanding the structure and function of catalytic RNA. Crystal structures of several ribozymes have provided detailed insight into the folds of RNA molecules. Models of other biologically important RNAs have been constructed based on structural, phylogenetic, and biochemical data. However, many questions regarding the catalytic mechanisms of ribozymes remain. This review compares the structures and possible catalytic mechanisms of four small self-cleaving RNAs: the hammerhead, hairpin, hepatitis delta virus, and in vitro-selected lead-dependent ribozymes. The organization of these small catalysts is contrasted to that of larger ribozymes, such as the group I intron.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.biophys.30.1.457
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 83
    Electronic Resource
    Electronic Resource
    MAGNETIC RESONANCE STUDIES OF THE BACTERIORHODOPSIN PUMP CYCLE (2002)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 31 (2002), S. 73-95 
    Details
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Active transport requires the alternation of substrate uptake and release with a switch in the access of the substrate binding site to the two sides of the membrane. Both the transfer and switch aspects of the photocycle have been subjects of magnetic resonance studies in bacteriorhodopsin. The results for ion transfer indicate that the Schiff base of the chromophore is hydrogen bonded before, during, and after its deprotonation. This suggests that the initial complex counterion of the Schiff base decomposes in such a way that the Schiff base carries its immediate hydrogen-bonding partner with it as it rotates during the first half of the photocycle. If so, bacteriorhodopsin acts as an inward-directed hydroxide pump rather than as an outward-directed proton pump. The studies of the access switch explore both protein-based and chromophore-based mechanisms. Combined with evidence from functional studies of mutants and other forms of spectroscopy, the results suggest that maintaining access to the extracellular side of the protein after photoisomerization involves twisting of the chromophore and that the decisive switch in access to the cytoplasmic side results from relaxation of the chromophore when the constraints on the Schiff base are released by decomposition of the complex counterion.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.biophys.31.082901.134233
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 84
    Electronic Resource
    Electronic Resource
    PIP2 AND PROTEINS: Interactions, Organization, and Information Flow (2002)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 31 (2002), S. 151-175 
    Details
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract We review the physical properties of phosphatidylinositol 4,5-bisphosphate (PIP2) that determine both its specific interactions with protein domains of known structure and its nonspecific electrostatic sequestration by unstructured domains. Several investigators have postulated the existence of distinct pools of PIP2 within the cell to account for the myriad functions of this lipid. Recent experimental work indicates certain regions of the plasma membrane-membrane ruffles and nascent phagosomes-do indeed concentrate PIP2. We consider two mechanisms that could account for this phenomenon: local synthesis and electrostatic sequestration. We conclude by considering the hypothesis that proteins such as MARCKS bind a significant fraction of the PIP2 in a cell, helping to sequester it in lateral membrane domains, then release this lipid in response to local signals such as an increased concentration of Ca++/calmodulin or activation of protein kinase C.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.biophys.31.082901.134259
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 85
    Electronic Resource
    Electronic Resource
    STRUCTURAL AND THERMODYNAMIC CORRELATES OF T CELL SIGNALING (2002)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 31 (2002), S. 121-149 
    Details
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract The first crystal structures of intact T cell receptors (TCRs) bound to class I peptide-MHC (pMHCs) antigens were determined in 1996. Since then, further structures of class I TCR/pMHC complexes have explored the degree of structural variability in the TCR-pMHC system and the structural basis for positive and negative selection. The recent determination of class II and allogeneic class I TCR/pMHC structures, as well as those of accessory molecules (e.g., CD3), has pushed our knowledge of TCR/pMHC interactions into new realms, shedding light on clinical pathologies, such as graft rejection and graft-versus-host disease. Furthermore, the determination of coreceptor structures lays the foundation for a more comprehensive structural description of the supramolecular TCR signaling events and those assemblies that arise in the immunological synapse. While these telling photodocumentaries of the TCR/pMHC interaction are composed mainly from static crystal structures, a full description of the biological snapshots in T cell signaling requires additional analytical methods that record the dynamics of the process. To this end, surface plasmon resonance (SPR), isothermal titration calorimetry (ITC), and ultracentrifugation (UC) have furnished both affinities and kinetics of the TCR/pMHC association. In the past year, structural, biochemical, and molecular biological data describing TCR/pMHC interactions have sublimely coalesced into a burgeoning well of understanding that promises to deliver further insights into T cell recognition. The coming years will, through a more intimate union of structural and kinetic data, allow many pressing questions to be addressed, such as how TCR/pMHC ligation is affected by coreceptor binding and what is the mechanism of TCR signaling in both early and late stages of T cell engagement with antigen-presenting cells.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.biophys.31.082901.134423
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 86
    Electronic Resource
    Electronic Resource
    THE alpha-HELIX AND THE ORGANIZATION AND GATING OF CHANNELS (2002)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 31 (2002), S. 207-233 
    Details
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract The structures of an increasing number of channels and other alpha-helical membrane proteins have been determined recently, including the KcsA potassium channel, the MscL mechanosensitive channel, and the AQP1 and GlpF members of the aquaporin family. In this chapter, the orientation and packing characteristics of bilayer-spanning helices are surveyed in integral membrane proteins. In the case of channels, alpha-helices create the sealed barrier that separates the hydrocarbon region of the bilayer from the permeation pathway for solutes. The helices surrounding the permeation pathway tend to be rather steeply tilted relative to the membrane normal and are consistently arranged in a right-handed bundle. The helical framework further provides a supporting scaffold for nonmembrane-spanning structures associated with channel selectivity. Although structural details remain scarce, the conformational changes associated with gating transitions between closed and open states of channels are reviewed, emphasizing the potential roles of helix-helix interactions in this process.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.biophys.31.082901.134329
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 87
    Electronic Resource
    Electronic Resource
    PRINCIPLES AND BIOPHYSICAL APPLICATIONS OF LANTHANIDE-BASED PROBES (2002)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 31 (2002), S. 275-302 
    Details
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Using luminescent lanthanides, instead of conventional fluorophores, as donor molecules in resonance energy transfer measurements offers many technical advantages and opens up a wide range of new applications. Advantages include farther measurable distances (~100 A) with greater accuracy, insensitivity to incomplete labeling, and the ability to use generic relatively large labels, when necessary. Applications highlighted include the study of ion channels in living cells, protein-protein interaction in cells, DNA-protein complexes, and high-throughput screening assays to measure peptide dimerization associated with DNA transcription factors and ligand-receptor interactions.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.biophys.31.101101.140927
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 88
    Electronic Resource
    Electronic Resource
    SINGLE-PARTICLE IMAGING OF MACROMOLECULES BY CRYO-ELECTRON MICROSCOPY (2002)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 31 (2002), S. 303-319 
    Details
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Cryo-electron microscopy (cryo-EM) of biological molecules in single-particle (i.e., unordered, nonaggregated) form is a new approach to the study of molecular assemblies, which are often too large and flexible to be amenable to X-ray crystallography. New insights into biological function on the molecular level are expected from cryo-EM applied to the study of such complexes "trapped" at different stages of their conformational changes and dynamical interactions. Important molecular machines involved in the fundamental processes of transcription, mRNA splicing, and translation are examples for successful applications of the new technique, combined with structural knowledge gained by conventional techniques of structure determination, such as X-ray crystallography and NMR.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.biophys.31.082901.134202
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 89
    Electronic Resource
    Electronic Resource
    RHODOPSIN: Insights from Recent Structural Studies (2002)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 31 (2002), S. 443-484 
    Details
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract The recent report of the crystal structure of rhodopsin provides insights concerning structure-activity relationships in visual pigments and related G protein-coupled receptors (GPCRs). The seven transmembrane helices of rhodopsin are interrupted or kinked at multiple sites. An extensive network of interhelical interactions stabilizes the ground state of the receptor. The ligand-binding pocket of rhodopsin is remarkably compact, and several chromophore-protein interactions were not predicted from mutagenesis or spectroscopic studies. The helix movement model of receptor activation, which likely applies to all GPCRs of the rhodopsin family, is supported by several structural elements that suggest how light-induced conformational changes in the ligand-binding pocket are transmitted to the cytoplasmic surface. The cytoplasmic domain of the receptor includes a helical domain extending from the seventh transmembrane segment parallel to the bilayer surface. The cytoplasmic surface appears to be approximately large enough to bind to the transducin heterotrimer in a one-to-one complex. The structural basis for several unique biophysical properties of rhodopsin, including its extremely low dark noise level and high quantum efficiency, can now be addressed using a combination of structural biology and various spectroscopic methods. Future high-resolution structural studies of rhodopsin and other GPCRs will form the basis to elucidate the detailed molecular mechanism of GPCR-mediated signal transduction.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.biophys.31.082901.134348
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 90
    Electronic Resource
    Electronic Resource
    CONFORMATIONAL REGULATION OF INTEGRIN STRUCTURE AND FUNCTION (2002)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 31 (2002), S. 485-516 
    Details
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Integrins are a structurally elaborate family of heterodimers that mediate divalent cation-dependent cell adhesion in a wide range of biological contexts. The inserted (I) domain binds ligand in the subset of integrins in which it is present. Its structure has been determined in two alternative conformations, termed open and closed. In striking similarity to signaling G proteins, rearrangement of a Mg2+-binding site is linked to large conformational movements in distant backbone regions. Mutations have been used to stabilize either the closed or open structures. These show that the snapshots of the open conformation seen only in the presence of a ligand or a ligand mimetic represent a high-affinity, ligand-binding conformation, whereas those of the closed conformation correspond to a low-affinity conformation. The C-terminal alpha-helix moves 10 A down the side of the domain in the open conformation. Locking in the conformation of the preceding loop is sufficient to increase affinity for ligand 9000-fold. This C-terminal "bell-rope" provides a mechanism for linkage to conformational movements in other domains. The transition from the closed to open conformation has been implicated in fast (〈1 s) regulation of integrin affinity in response to activation signals from inside the cell. Recent integrin structures and functional studies reveal interactions between beta-propeller, I, and I-like domains in the headpiece, and a critical role for integrin EGF domains in the stalk region. These studies suggest that the headpiece of the integrin faces down toward the membrane in the inactive conformation and extends upward in a "switchblade"-like opening motion upon activation. These long-range structural rearrangements of the entire integrin molecule involving multiple interdomain contacts appear closely linked to conformational changes in the I domain, which result in increased affinity and competence for ligand binding.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.biophys.31.101101.140922
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 91
    Electronic Resource
    Electronic Resource
    OPTICAL SINGLE TRANSPORTER RECORDING: Transport Kinetics in Microarrays of Membrane Patches (2003)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 32 (2003), S. 47-67 
    Details
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Optical single transporter recording (OSTR) is an emerging technique for the fluorescence microscopic measurement of transport kinetics in membrane patches. Membranes are attached to transparent microarrays of cylindrical test compartments (TCs) ~0.1-100 mum in diameter and ~10-100 mum in depth. Transport across membrane patches that may contain single transporters or transporter populations is recorded by confocal microscopy. By these means transport of proteins through single nuclear pore complexes has been recorded at rates of 〈1 translocation/s. In addition to the high sensitivity in terms of measurable transport rates OSTR features unprecedented spatial selectivity and parallel processing. This article reviews the conceptual basis of OSTR and its realization. Applications to nuclear transport are summarized. The further development of OSTR is discussed and its extension to a diversity of transporters, including translocases and ATP-binding cassette (ABC) pumps, projected.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.biophys.32.110601.142429
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 92
    Electronic Resource
    Electronic Resource
    STRUCTURE AND FUNCTION OF NATURAL KILLER CELL SURFACE RECEPTORS* (2003)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 32 (2003), S. 93-114 
    Details
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Since mid-1990, with cloning and identification of several families of natural killer (NK) receptors, research on NK cells began to receive appreciable attention. Determination of structures of NK cell surface receptors and their ligand complexes led to a fast growth in our understanding of the activation and ligand recognition by these receptors as well as their function in innate immunity. Functionally, NK cell surface receptors are divided into two groups, the inhibitory and the activating receptors. Structurally, they belong to either the immunoglobulin (Ig)-like receptor superfamily or the C-type lectin-like receptor (CTLR) superfamily. Their ligands are either members of class I major histocompatibility complexes (MHC) or homologs of class I MHC molecules. The inhibitory form of NK receptors provides the protective immunity through recognizing class I MHC molecules with self-peptides on healthy host cells. The activating, or the noninhibitory, NK receptors mediate the killing of tumor or virally infected cells through their specific ligand recognition. The structures of activating and inhibitory NK cell surface receptors and their complexes with the ligands determined to date, including killer immunoglobulin-like receptors (KIRs) and their complexes with HLA molecules, CD94, Ly49A, and its complex with H-2Dd, and NKG2D receptors and their complexes with class I MHC homologs, are reviewed here.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.biophys.32.110601.142347
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 93
    Electronic Resource
    Electronic Resource
    THE POWER AND PROSPECTS OF FLUORESCENCE MICROSCOPIES AND SPECTROSCOPIES (2003)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 32 (2003), S. 161-182 
    Details
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Recent years have witnessed a renaissance of fluorescence microscopy techniques and applications, from live-animal multiphoton confocal microscopy to single-molecule fluorescence spectroscopy and imaging in living cells. These achievements have been made possible not so much because of improvements in microscope design, but rather because of development of new detectors, accessible continuous wave and pulsed laser sources, sophisticated multiparameter analysis on one hand, and the development of new probes and labeling chemistries on the other. This review tracks the lineage of ideas and the evolution of thinking that have led to the actual developments, and presents a comprehensive overview of the field, with emphasis put on our laboratory's interest in single-molecule microscopy and spectroscopy.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.biophys.32.110601.142525
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 94
    Electronic Resource
    Electronic Resource
    NEW INSIGHT INTO SITE-SPECIFIC RECOMBINATION FROM FLP RECOMBINASE-DNA STRUCTURES (2003)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 32 (2003), S. 135-159 
    Details
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract The lamba integrase, or tyrosine-based family of site-specific recombinases, plays an important role in a variety of biological processes by inserting, excising, and inverting DNA segments. Flp, encoded by the yeast 2-mum plasmid, is the best-characterized eukaryotic member of this family and is responsible for maintaining the copy number of this plasmid. Over the past several years, structural and biochemical studies have shed light on the details of a common catalytic scheme utilized by these enzymes with interesting variations under different biological contexts. The emergence of new Flp structures and solution data provides insights not only into its unique mechanism of active site assembly and activity regulation but also into the specific contributions of certain protein residues to catalysis.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.biophys.32.110601.141732
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 95
    Electronic Resource
    Electronic Resource
    X-RAY CRYSTALLOGRAPHIC ANALYSIS OF LIPID-PROTEIN INTERACTIONS IN THE BACTERIORHODOPSIN PURPLE MEMBRANE* (2003)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 32 (2003), S. 285-310 
    Details
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract The past decade has witnessed increasingly detailed insights into the structural mechanism of the bacteriorhodopsin photocycle. Concurrently, there has been much progress within our knowledge pertaining to the lipids of the purple membrane, including the discovery of new lipids and the overall effort to localize and identify each lipid within the purple membrane. Therefore, there is a need to classify this information to generalize the findings. We discuss the properties and roles of haloarchaeal lipids and present the structural data as individual case studies. Lipid-protein interactions are discussed in the context of structure-function relationships. A brief discussion of the possibility that bacteriorhodopsin functions as a light-driven inward hydroxide pump rather than an outward proton pump is also presented.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.biophys.32.110601.142516
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 96
    Electronic Resource
    Electronic Resource
    THE CRYSTALLOGRAPHIC MODEL OF RHODOPSIN AND ITS USE IN STUDIES OF OTHER G PROTEIN-COUPLED RECEPTORS (2003)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 32 (2003), S. 375-397 
    Details
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract G protein-coupled receptors (GPCRs) are integral membrane proteins that respond to environmental signals and initiate signal transduction pathways activating cellular processes. Rhodopsin is a GPCR found in rod cells in retina where it functions as a photopigment. Its molecular structure is known from cryo-electron microscopic and X-ray crystallographic studies, and this has reshaped many structure/function questions important in vision science. In addition, this first GPCR structure has provided a structural template for studies of other GPCRs, including many known drug targets. After presenting an overview of the major structural elements of rhodopsin, recent literature covering the use of the rhodopsin structure in analyzing other GPCRs will be summarized. Use of the rhodopsin structural model to understand the structure and function of other GPCRs provides strong evidence validating the structural model.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.biophys.32.110601.142520
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 97
    Electronic Resource
    Electronic Resource
    PROTEOME ANALYSIS BY MASS SPECTROMETRY* (2003)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 32 (2003), S. 399-424 
    Details
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract The coupling of high-performance mass spectrometry instrumentation with highly efficient chromatographic and electrophoretic separations has enabled rapid qualitative and quantitative analysis of thousands of proteins from minute samples of biological materials. Here, we review recent progress in the development and application of mass spectrometry-based techniques for the qualitative and quantitative analysis of global proteome samples derived from whole cells, tissues, or organisms. Techniques such as multidimensional peptide and protein separations coupled with mass spectrometry, accurate mass measurement of peptides from global proteome digests, and mass spectrometric characterization of intact proteins hold great promise for characterization of highly complex protein mixtures. Advances in chemical tagging and isotope labeling techniques have enabled quantitative analysis of proteomes, and highly specific isolation strategies have been developed aimed at selective analysis of posttranslationally modified proteins.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.biophys.32.110601.141854
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 98
    Electronic Resource
    Electronic Resource
    RESIDUAL DIPOLAR COUPLINGS IN NMR STRUCTURE ANALYSIS*1 (2004)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 33 (2004), S. 387-413 
    Details
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Residual dipolar couplings (RDCs) have recently emerged as a new tool in nuclear magnetic resonance (NMR) with which to study macromolecular structure and function in a solution environment. RDCs are complementary to the more conventional use of NOEs to provide structural information. While NOEs are local-distance restraints, RDCs provide long-range orientational information. RDCs are now widely utilized in structure calculations. Increasingly, they are being used in novel applications to address complex issues in structural biology such as the accurate determination of the global structure of oligonucleotides and the relative orientation of protein domains. This review briefly describes the theory and methods for obtaining RDCs and then describes the range of biological applications where RDCs have been used.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.biophys.33.110502.140306
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 99
    Electronic Resource
    Electronic Resource
    MODEL SYSTEMS, LIPID RAFTS, AND CELL MEMBRANES1 (2004)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 33 (2004), S. 269-295 
    Details
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Views of how cell membranes are organized are presently changing. The lipid bilayer that constitutes these membranes is no longer understood to be a homogeneous fluid. Instead, lipid assemblies, termed rafts, have been introduced to provide fluid platforms that segregate membrane components and dynamically compartmentalize membranes. These assemblies are thought to be composed mainly of sphingolipids and cholesterol in the outer leaflet, somehow connected to domains of unknown composition in the inner leaflet. Specific classes of proteins are associated with the rafts. This review critically analyzes what is known of phase behavior and liquid-liquid immiscibility in model systems and compares these data with what is known of domain formation in cell membranes.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.biophys.32.110601.141803
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 100
    Electronic Resource
    Electronic Resource
    SALMONELLA INTERACTIONS WITH HOST CELLS: Type III Secretion at Work (2001)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Cell and Developmental Biology 17 (2001), S. 53-86 
    Details
    ISSN: 1081-0706
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: Abstract The bacterial pathogen Salmonella enterica has evolved a very sophisticated functional interface with its vertebrate hosts. At the center of this interface is a specialized organelle, the type III secretion system, that directs the translocation of bacterial proteins into the host cell. Salmonella spp. encode two such systems that deliver a remarkable array of bacterial proteins capable of modulating a variety of cellular functions, including actin cytoskeleton dynamics, nuclear responses, and endocytic trafficking. Many of these bacterial proteins operate by faithful mimicry of host proteins, in some cases representing the result of extensive molecular tinkering and convergent evolution. The coordinated action of these type III secreted proteins secures the replication and survival of the bacteria avoiding overt damage to the host. The study of this remarkable pathogen is not only illuminating general paradigms in microbial pathogenesis but is also providing valuable insight into host cell functions.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.cellbio.17.1.53
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
Close ⊗
This website uses cookies and the analysis tool Matomo. More information can be found here...